Isolated human protease proteins, nucleic acid molecules encoding human protease proteins, and uses thereof

ABSTRACT

The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the protease peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the protease peptides, and methods of identifying modulators of the protease peptides.

FIELD OF THE INVENTION

[0001] The present invention is in the field of protease proteins thatare related to the hepsin protease subfamily, recombinant DNA molecules,and protein production. The present invention specifically providesnovel peptides and proteins that effect proteincleavage/processing/turnover and nucleic acid molecules encoding suchpeptide and protein molecules, all of which are useful in thedevelopment of human therapeutics and diagnostic compositions andmethods.

BACKGROUND OF THE INVENTION

[0002] The proteases may be categorized into families by the differentamino acid sequences (generally between 2 and 10 residues) located oneither side of the cleavage site of the protease.

[0003] The proper functioning of the cell requires careful control ofthe levels of important structural proteins, enzymes, and regulatoryproteins. One of the ways that cells can reduce the steady state levelof a particular protein is by proteolytic degradation. Further, one ofthe ways cells produce functioning proteins is to produce pre orpro-protein precursors that are processed by proteolytic degradation toproduce an active moiety. Thus, complex and highly-regulated mechanismshave been evolved to accomplish this degradation.

[0004] Proteases regulate many different cell proliferation,differentiation, and signaling processes by regulating protein turnoverand processing. Uncontrolled protease activity (either increased ordecreased) has been implicated in a variety of disease conditionsincluding inflammation, cancer, arteriosclerosis, and degenerativedisorders.

[0005] An additional role of intracellular proteolysis is in thestress-response. Cells that are subject to stress such as starvation,heat-shock, chemical insult or mutation respond by increasing the ratesof proteolysis. One function of this enhanced proteolysis is to salvageamino acids from non-essential proteins. These amino acids can then bere-utilized in the synthesis of essential proteins or metabolizeddirectly to provide energy. Another function is in the repair of damagecaused by the stress. For example, oxidative stress has been shown todamage a variety of proteins and cause them to be rapidly degraded.

[0006] The International Union of Biochemistry and Molecular Biology(IUBMB) has recommended to use the term peptidase for the subset ofpeptide bond hydrolases (Subclass E.C 3.4.). The widely used termprotease is synonymous with peptidase. Peptidases comprise two groups ofenzymes: the endopeptidases and the exopeptidases, which cleave peptidebonds at points within the protein and remove amino acids sequentiallyfrom either N or C-terminus respectively. The term proteinase is alsoused as a synonym word for endopeptidase and four mechanistic classes ofproteinases are recognized by the IUBMB: two of these are describedbelow (also see: Handbook of Proteolytic Enzymes by Barrett, Rawlings,and Woessner A P Press, NY 1998). Also, for a review of the various usesof proteases as drug targets, see: Weber M, Emerging treatments forhypertension: potential role for vasopeptidase inhibition; Am JHypertens November 1999;12(11 Pt 2):139s⁻¹⁴⁷S; Kentsch M, Otter W, Novelneurohormonal modulators in cardiovascular disorders. The therapeuticpotential of endopeptidase inhibitors, Drugs R D April 1999;1(4):331-8;Scarborough R M, Coagulation factor Xa: the prothrombinase complex as anemerging therapeutic target for small molecule inhibitors, J Enzym Inhib1998;14(1):15-25; Skotnicki JS, et al., Design and syntheticconsiderations of matrix metalloproteinase inhibitors, Ann N Y Acad SciJun. 30, 1999;878:61-72; McKerrow J H, Engel J C, Caffrey C R, Cysteineprotease inhibitors as chemotherapy for parasitic infections, Bioorg MedChem April 1999;7(4):639-44; Rice K D, Tanaka R D, Katz B A, Numerof RP, Moore W R, Inhibitors of tryptase for the treatment of mastcell-mediated diseases, Curr Pharm Des October 1998;4(5):381-96;Materson B J, Will angiotensin converting enzyme genotype, receptormutation identification, and other miracles of molecular biology permitreduction of NNT Am J Hypertens August 1998;11(8 Pt 2):138S-142S

[0007] Serine Proteases

[0008] The serine proteases (SP) are a large family of proteolyticenzymes that include the digestive enzymes, trypsin and chymotrypsin,components of the complement cascade and of the blood-clotting cascade,and enzymes that control the degradation and turnover of macromoleculesof the extracellular matrix. SP are so named because of the presence ofa serine residue in the active catalytic site for protein cleavage. SPhave a wide range of substrate specificities and can be subdivided intosubfamilies on the basis of these specificities. The main sub-familiesare trypases (cleavage after arginine or lysine), aspases (cleavageafter aspartate), chyrnases (cleavage after phenylalanine or leucine),metases (cleavage after methionine), and serases (cleavage afterserine).

[0009] A series of six SP have been identified in murine cytotoxicT-lymphocytes (CTL) and natural killer (NK) cells. These SP are involvedwith CTL and NK cells in the destruction of virally transformed cellsand tumor cells and in organ and tissue transplant rejection (Zunino, S.J. et al. (1990) J. Immunol. 144:2001-9; Sayers, T. J. et al. (1994) J.Immunol. 152:2289-97). Human homologs of most of these enzymes have beenidentified (Trapani, J. A. et al. (1988) Proc. Natl. Acad. Sci.85:6924-28; Caputo, A. et al. (1990) J. Immunol. 145:737-44). Like allSP, the CTL-SP share three distinguishing features: 1) the presence of acatalytic triad of histidine, serine, and aspartate residues whichcomprise the active site; 2) the sequence GDSGGP which contains theactive site serine; and 3) an N-terminal IIGG sequence whichcharacterizes the mature SP.

[0010] The SP are secretory proteins which contain N-terminal signalpeptides that serve to export the immature protein across theendoplasmic reticulum and are then cleaved (von Heijne (1986) Nuc. Acid.Res. 14:5683-90). Differences in these signal sequences provide onemeans of distinguishing individual SP. Some SP, particularly thedigestive enzymes, exist as inactive precursors or preproenzymes, andcontain a leader or activation peptide sequence 3′ of the signalpeptide. This activation peptide may be 2-12 amino acids in length, andit extends from the cleavage site of the signal peptide to theN-terminal IIGG sequence of the active, mature protein. Cleavage of thissequence activates the enzyme. This sequence varies in different SPaccording to the biochemical pathway and/or its substrate (Zunino et al,supra; Sayers et al, supra). Other features that distinguish various SPare the presence or absence of N-linked glycosylation sites that providemembrane anchors, the number and distribution of cysteine residues thatdetermine the secondary structure of the SP, and the sequence of asubstrate binding sites such as S′. The S′ substrate binding region isdefined by residues extending from approximately +17 to +29 relative tothe N-terminal I (+1). Differences in this region of the molecule arebelieved to determine SP substrate specificities (Zunino et al, supra).

[0011] Trypsinogens

[0012] The trypsinogens are serine proteases secreted by exocrine cellsof the pancreas (Travis J and Roberts R. Biochemistry 1969; 8: 2884-9;Mallory P and Travis J, Biochemistry 1973; 12: 2847-51). Two major typesof trypsinogen isoenzymes have been characterized, trypsinogen-1, alsocalled cationic trypsinogen, and trypsinogen-2 or anionic trypsinogen.The trypsinogen proenzymes are activated to trypsins in the intestine byenterokinase, which removes an activation peptide from the N-terminus ofthe trypsinogens. The trypsinogens show a high degree of sequencehomology, but they can be separated on the basis of charge differencesby using electrophoresis or ion exchange chromatography. The major formof trypsinogen in the pancreas and pancreatic juice is trypsinogen-1(Guy C O et al., Biochem Biophys Res Commun 1984; 125: 516-23). In serumof healthy subjects, trypsinogen-1 is also the major form, whereas inpatients with pancreatitis, trypsinogen-2 is more strongly elevated(Itkonen et al., J Lab Clin Med 1990; 115:712-8). Trypsinogens alsooccur in certain ovarian tumors, in which trypsinogen-2 is the majorform (Koivunen et al., Cancer Res 1990; 50: 2375-8). Trypsin-1 incomplex with alpha-1-antitrypsin, also called alpha-1-antiprotease, hasbeen found to occur in serum of patients with pancreatitis (Borgstrom Aand Ohlsson K, Scand J Clin Lab Invest 1984; 44: 381-6) butdetermination of this complex has not been found useful fordifferentiation between pancreatic and other gastrointestinal diseases(Borgstrom et al., Scand J Clin Lab Invest 1989; 49:757-62).

[0013] Trypsinogen-1 and -2 are closely related immunologically (Kimlandet al., Clin Chim Acta 1989; 184: 31-46; Itkonen et al., 1990), but byusing monoclonal antibodies (Itkonen et al., 1990) or by absorbingpolyclonal antisera (Kimland et al., 1989) it is possible to obtainreagents enabling specific measurement of each form of trypsinogen.

[0014] When active trypsin reaches the blood stream, it is inactivatedby the major trypsin inhibitors alpha-2-macroglobulin andalpha-1-antitrypsin (AAT). AAT is a 58 kilodalton serine proteaseinhibitor synthesized in the liver and is one of the main proteaseinhibitors in blood. Whereas complexes between trypsin-1 and AAT aredetectable in serum (Borgstrom and Ohlsson, 1984) the complexes withalpha-2macroglobulin are not measurable with antibody-based assays(Ohlsson K, Acta Gastroenterol Belg 1988; 51: 3-12).

[0015] Inflammation of the pancreas or pancreatitis may be classified aseither acute or chronic by clinical criteria. With treatment, acutepancreatitis can often be cured and normal function restored. Chronicpancreatitis often results in permanent damage. The precise mechanismswhich trigger acute inflammation are not understood. However, somecauses in the order of their importance are alcohol ingestion, biliarytract disease, post-operative trauma, and hereditary pancreatitis. Onetheory provides that autodigestion, the premature activation ofproteolytic enzymes in the pancreas rather than in the duodenum, causesacute pancreatitis. Any number of other factors including endotoxins,exotoxins, viral infections, ischemia, anoxia, and direct trauma mayactivate the proenzymes. In addition, any internal or external blockageof pancreatic ducts can also cause an accumulation of pancreatic juicesin the pancreas resulting cellular damage.

[0016] Anatomy, physiology, and diseases of the pancreas are reviewed,inter alia, in Guyton A C (1991) Textbook of Medical Physiology, W BSaunders Co, Philadelphia Pa.; Isselbacher K J et al (1994) Harrison'sPrinciples of Internal Medicine, McGraw-Hill, New York City; Johnson K E(1991) Histology and Cell Biology, Harwal Publishing, Media Pa.; and TheMerck Manual of Diagnosis and Therapy (1992) Merck ResearchLaboratories, Rahway N.J.

[0017] Metalloprotease

[0018] The metalloproteases may be one of the older classes ofproteinases and are found in bacteria, fungi as well as in higherorganisms. They differ widely in their sequences and their structuresbut the great majority of enzymes contain a zinc atom which iscatalytically active. In some cases, zinc may be replaced by anothermetal such as cobalt or nickel without loss of the activity. Bacterialthermolysin has been well characterized and its crystallographicstructure indicates that zinc is bound by two histidines and oneglutamic acid. Many enzymes contain the sequence HEXXH, which providestwo histidine ligands for the zinc whereas the third ligand is either aglutamic acid (thermolysin, neprilysin, alanyl aminopeptidase) or ahistidine (astacin). Other families exhibit a distinct mode of bindingof the Zn atom. The catalytic mechanism leads to the formation of a noncovalent tetrahedral intermediate after the attack of a zinc-bound watermolecule on the carbonyl group of the scissile bond. This intermediateis further decomposed by transfer of the glutamic acid proton to theleaving group.

[0019] Metalloproteases contain a catalytic zinc metal center whichparticipates in the hydrolysis of the peptide backbone (reviewed inPower and Harper, in Protease Inhibitors, A. J. Barrett and G. Salversen(eds.) Elsevier, Amsterdam, 1986, p. 219). The active zinc centerdifferentiates some of these proteases from calpains and trypsins whoseactivities are dependent upon the presence of calcium. Examples ofmetalloproteases include carboxypeptidase A, carboxypeptidase B, andthermolysin.

[0020] Metalloproteases have been isolated from a number of procaryoticand eucaryotic sources, e.g. Bacillus subtilis (McConn et al., 1964, J.Biol. Chem. 239:3706); Bacillus megaterium; Serratia (Miyata et al.,1971, Agr. Biol. Chem. 35:460); Clostridium bifermentans (MacFarlane etal., 1992, App. Environ. Microbiol. 58:1195-1200), Legionellapneumophila (Moffat et al., 1994, Infection and Immunity 62:751-3). Inparticular, acidic metalloproteases have been isolated from broad-bandedcopperhead venoms (Johnson and Ownby, 1993, Int. J. Biochem.25:267-278), rattlesnake venoms (Chlou et al., 1992, Biochem. Biophys.Res. Commun. 187:389-396) and articular cartilage (Treadwell et al.,1986, Arch. Biochem. Biophys. 251:715-723). Neutral metalloproteases,specifically those having optimal activity at neutral pH have, forexample, been isolated from Aspergillus sojae (Sekine, 1973, Agric.Biol. Chem. 37:1945-1952). Neutral metalloproteases obtained fromAspergillus have been classified into two groups, npI and npII (Sekine,1972, Agric. Biol. Chem. 36:207-216). So far, success in obtaining aminoacid sequence information from these fungal neutral metalloproteases hasbeen limited. An npII metalloprotease isolated from Aspergillus oryzaehas been cloned based on amino acid sequence presented in the literature(Tatsumi et al., 1991, Mol. Gen. Genet. 228:97-103). However, to date,no npI fungal metalloprotease has been cloned or sequenced. Alkalinemetalloproteases, for example, have been isolated from Pseudomonasaeruginosa (Baumann et al., 1993, EMBO J 12:3357-3364) and the insectpathogen Xenorhabdus luminescens (Schmidt et al., 1998, Appl. Environ.Microbiol. 54:2793-2797).

[0021] Metalloproteases have been devided into several distinct familiesbased primarily on activity and sturcture: 1) water nucleophile; waterbound by single zinc ion ligated to two His (within the motif HEXXH) andGlu, His or Asp; 2) water nucleophile; water bound by single zinc ionligated to His, Glu (within the motif HXXE) and His; 3) waternucleophile; water bound by single zinc ion ligated to His, Asp and His;4) Water nucleophile; water bound by single zinc ion ligated to two His(within the motif HXXEH) and Glu and 5) water nucleophile; water boundby two zinc ions ligated by Lys, Asp, Asp, Asp, Glu.

[0022] Examples of members of the metalloproteinase family include, butare not limited to, membrane alanyl aminopeptidase (Homo sapiens),germinal peptidyl-dipeptidase A (Homo sapiens), thimet oligopeptidase(Rattus norvegicus), oligopeptidase F (Lactococcus lactis), mycolysin(Streptomyces cacaoi), immune inhibitor A (Bacillus thuringiensis),snapalysin (Streptomyces lividans), leishmanolysin (Leishmania major),microbial collagenase (Vibrio alginolyticus), microbial collagenase,class I (Clostridium perfringens), collagenase 1 (Homo sapiens),serralysin (Serratia marcescens), fragilysin (Bacteroides fragilis),gametolysin (Chlamydomonas reinhardtii), astacin (Astacus fluviatilis),adamalysin (Crotalus adamanteus), ADAM 10 (Bos taurus), neprilysin (Homosapiens), carboxypeptidase A (Homo sapiens), carboxypeptidase E (Bostaurus), gamma-D-glutamyl-(L)-meso-diaminopimelate peptidase I (Bacillussphaericus), vanY D-Ala-D-Ala carboxypeptidase (Enterococcus faecium),endolysin (bacteriophage A118), pitrilysin (Escherichia coli),mitochondrial processing peptidase (Saccharomyces cerevisiae), leucylaminopeptidase (Bos taurus), aminopeptidase I (Saccharomycescerevisiae), membrane dipeptidase (Homo sapiens), glutamatecarboxypeptidase (Pseudomonas sp.), Gly-X carboxypeptidase(Saccharomyces cerevisiae), O-sialoglycoprotein endopeptidase(Pasteurella haemolytica), beta-lytic metalloendopeptidase(Achromobacter lyticus), methionyl aminopeptidase I (Escherichia coli),X-Pro aminopeptidase (Escherichia coli), X-His dipeptidase (Escherichiacoli), IgA1-specific metalloendopeptidase (Streptococcus sanguis),tentoxilysin (Clostridium tetani), leucyl aminopeptidase (Vibrioproteolyticus), aminopeptidase (Streptomyces griseus), IAPaminopeptidase (Escherichia coli), aminopeptidase T (Thermus aquaticus),hyicolysin (Staphylococcus hyicus), carboxypeptidase Taq (Thermusaquaticus), anthrax lethal factor (Bacillus anthracis), penicillolysin(Penicillium citrinum), fungalysin (Aspergillus fumigatus), lysostaphin(Staphylococcus simulans), beta-aspartyl dipeptidase (Escherichia coli),carboxypeptidase Ss1 (Sulfolobus solfataricus), FtsH endopeptidase(Escherichia coli), glutamyl aminopeptidase (Lactococcus lactis),cytophagalysin (Cytophaga sp.), metalloendopeptidase (vaccinia virus),VanX D-Ala-D-Ala dipeptidase (Enterococcus faecium), Ste24pendopeptidase (Saccharomyces cerevisiae), dipeptidyl-peptidase III(Rattus norvegicus), S2P protease (Homo sapiens), sporulation factorSpoIVFB (Bacillus subtilis), and HYBD endopeptidase (Escherichia coli).

[0023] Metalloproteases have been found to have a number of uses. Forexample, there is strong evidence that a metalloprotease is involved inthe in vivo proteolytic processing of the vasoconstrictor, endothelin-1.Rat metalloprotease has been found to be involved in peptide hormoneprocessing. One important subfamily of the metalloproteases are thematrix metalloproteases.

[0024] A number of diseases are thought to be mediated by excess orundesired metalloprotease activity or by an imbalance in the ratio ofthe various members of the protease family of proteins. These include:a) osteoarthritis (Woessner, et al., J. Biol. Chem. 259(6), 3633, 1984;Phadke, et al., J. Rheumatol. 10, 852, 1983), b) rheumatoid arthritis(Mullins, et al., Biochim. Biophys. Acta 695, 117, 1983; Woolley, etal., Arthritis Rheum. 20, 1231, 1977; Gravallese, et al., ArthritisRheum. 34, 1076, 1991), c) septic arthritis (Williams, et al., ArthritisRheum. 33, 533, 1990), d) tumor metastasis (Reich, et al., Cancer Res.48, 3307, 1988, and Matrisian, et al., Proc. Nat'l. Acad. Sci., USA 83,9413, 1986), e) periodontal diseases (Overall, et al., J. PeriodontalRes. 22, 81, 1987), f) corneal ulceration (Bums, et al., Invest.Opthalmol. Vis. Sci. 30, 1569, 1989), g) proteinuria (Baricos, et al.,Biochem. J. 254, 609, 1988), h) coronary thrombosis from atheroscleroticplaque rupture (Henney, et al., Proc. Nat'l. Acad. Sci., USA 88,8154-8158, 1991), i) aneurysmal aortic disease (Vine, et al., Clin. Sci.81, 233, 1991), j) birth control (Woessner, et al., Steroids 54, 491,1989), k) dystrophobic epidermolysis bullosa (Kronberger, et al., J.Invest. Dermatol. 79, 208, 1982), and 1) degenerative cartilage lossfollowing traumatic joint injury, m) conditions leading to inflammatoryresponses, osteopenias mediated by MMP activity, n) tempero mandibularjoint disease, o) demyelating diseases of the nervous system (Chantry,et al., J. Neurochem. 50, 688, 1988).

[0025] Aspartic Protease

[0026] Aspartic proteases have been divided into several distinctfamilies based primarily on activity and structure. These include 1)water nucleophile; water bound by two Asp from monomer or dimer; allendopeptidases, from eukaryote organisms, viruses or virus-likeorganisms and 2) endopeptidases that are water nucleophile and are waterbound by Asp and Asn.

[0027] Most of aspartic proteases belong to the pepsin family. Thepepsin family includes digestive enzymes such as pepsin and chymosin aswell as lysosomal cathepsins D and processing enzymes such as renin, andcertain fungal proteases (penicillopepsin, rhizopuspepsin,endothiapepsin). A second family comprises viral proteases such as theprotease from the AIDS virus (HIV) also called retropepsin.Crystallographic studies have shown that these enzymes are bilobedmolecules with the active site located between two homologous lobes.Each lobe contributes one aspartate residue of the catalytically activediad of aspartates. These two aspartyl residues are in close geometricproximity in the active molecule and one aspartate is ionized whereasthe second one is unionized at the optimum pH range of 2-3.Retropepsins, are monomeric, i.e carry only one catalytic aspartate andthen dimerization is required to form an active enzyme.

[0028] In contrast to serine and cysteine proteases, catalysis byaspartic protease do not involve a covalent intermediate though atetrahedral intermediate exists. The nucleophilic attack is achieved bytwo simultaneous proton transfer: one from a water molecule to the diadof the two carboxyl groups and a second one from the diad to thecarbonyl oxygen of the substrate with the concurrent CO—NH bondcleavage. This general acid-base catalysis, which may be called a“push-pull” mechanism leads to the formation of a non covalent neutraltetrahedral intermediate.

[0029] Examples of the aspartic protease family of proteins include, butare not limited to, pepsin A (Homo sapiens), HIV1 retropepsin (humanimmunodeficiency virus type 1), endopeptidase (cauliflower mosaicvirus), bacilliform virus putative protease (rice tungro bacilliformvirus), aspergillopepsin II (Aspergillus niger), thermopsin (Sulfolobusacidocaldarius), nodavirus endopeptidase (flock house virus),pseudomonapepsin (Pseudomonas sp. 101), signal peptidase II (Escherichiacoli), polyprotein peptidase (human spumaretrovirus), copia transposon(Drosophila melanogaster), SIRE-1 peptidase (Glycine max),retrotransposon bs1 endopeptidase (Zea mays), retrotransposon peptidase(Drosophila buzzatii), Tas retrotransposon peptidase (Ascarislumbricoides), Pao retrotransposon peptidase (Bombyx mori), putativeproteinase of Skippy retrotransposon (Fusarium oxysporum), tetravirusendopeptidase (Nudaurelia capensis omega virus), presenilin 1 (Homosapiens).

[0030] Proteases and Cancer

[0031] Proteases are critical elements at several stages in theprogression of metastatic cancer. In this process, the proteolyticdegradation of structural protein in the basal membrane allows forexpansion of a tumor in the primary site, evasion from this site as wellas homing and invasion in distant, secondary sites. Also, tumor inducedangiogenesis is required for tumor growth and is dependent onproteolytic tissue remodeling. Transfection experiments with varioustypes of proteases have shown that the matrix metalloproteases play adominant role in these processes in particular gelatinases A and B(MMP-2 and MMP-9, respectively). For an overview of this field seeMullins, et al., Biochim. Biophys. Acta 695, 177, 1983; Ray, et al.,Eur. Respir. J. 7, 2062, 1994; Birkedal-Hansen, et al., Crit. Rev. OralBiol. Med. 4, 197, 1993.

[0032] Furthermore, it was demonstrated that inhibition of degradationof extracellular matrix by the native matrix metalloprotease inhibitorTIMP-2 (a protein) arrests cancer growth (DeClerck, et al., Cancer Res.52, 701, 1992) and that TIMP-2 inhibits tumor-induced angiogenesis inexperimental systems (Moses, et al. Science 248, 1408, 1990). For areview, see DeClerck, et al., Ann. N.Y. Acad. Sci. 732, 222, 1994. Itwas further demonstrated that the synthetic matrix metalloproteaseinhibitor batimastat when given intraperitoneally inhibits human colontumor growth and spread in an orthotopic model in nude mice (Wang, etal. Cancer Res. 54, 4726, 1994) and prolongs the survival of micebearing human ovarian carcinoma xenografts (Davies, et. al., Cancer Res.53, 2087, 1993). The use of this and related compounds has beendescribed in Brown, et al., WO-9321942 A2.

[0033] There are several patents and patent applications claiming theuse of metalloproteinase inhibitors for the retardation of metastaticcancer, promoting tumor regression, inhibiting cancer cellproliferation, slowing or preventing cartilage loss associated withosteoarthritis or for treatment of other diseases as noted above (e.g.Levy, et al., WO-9519965 A1; Beckett, et al., WO-9519956 A1; Beckett, etal., WO-9519957 A1; Beckett, et al., WO-9519961 A1; Brown, et al.,WO-9321942 A2; Crimmin, et al., WO-9421625 A1; Dickens, et al., U.S.Pat. No. 4,599,361; Hughes, et al., U.S. Pat. No. 5,190,937; Broadhurst,et al., EP 574758 A1; Broadhurst, et al., EP 276436; and Myers, et al.,EP 520573 A1.

[0034] Hepsin

[0035] Extracellular proteases mediate the digestion of neighboringextracellular matrix components in initial tumor growth, allow sheddingor desquamation of tumor cells into the surrounding environment, providethe basis for invasion of basement membranes in target metastaticorgans, and are required for release and activation of many growth andangiogenic factors. Experimental evidence indicates that hepsin, a cellsurface serine protease identified in hepatoma cells, is overexpressedin ovarian cancer. Hepsin is a serine protease found in most tissues,abundant in the liver. It is a membrane associated protein and is notfound in the cytosol. Hepsin does not appear to be essential fordevelopment or homeostasis. On Northern blot analysis, the hepsintranscript was abundant in carcinoma but was almost never expressed innormal adult tissue, including normal ovary, suggesting that hepsin isfrequently overexpressed in ovarian tumors and therefore may be acandidate protease in the invasive process and growth capacity ofovarian tumor cells.

[0036] For more information, see: Tanimoto, et al., Cancer Res. Jul. 15,1997;57(14):2884-7; Leytus, et al., Biochemistry 27: 1067-1074, 1988,PubMed ID: 2835076; Tsuji, et al., J. Biol. Chem. 266: 16948-16953,1991, PubMed ID: 1885621; and Wu, Q., et al., J. Clin. Invest. 101:321-326, 1998, PubMed ID: 9435303.

[0037] Protease proteins, particularly members of the hepsin subfamily,are a major target for drug action and development. Accordingly, it isvaluable to the field of pharmaceutical development to identify andcharacterize previously unknown members of this subfamily of proteaseproteins. The present invention advances the state of the art byproviding a previously unidentified human protease proteins that havehomology to members of the hepsin subfamily.

SUMMARY OF THE INVENTION

[0038] The present invention is based in part on the identification ofamino acid sequences of human protease peptides and proteins that arerelated to the hepsin protease subfamily, as well as allelic variantsand other mammalian orthologs thereof. These unique peptide sequences,and nucleic acid sequences that encode these peptides, can be used asmodels for the development of human therapeutic targets, aid in theidentification of therapeutic proteins, and serve as targets for thedevelopment of human therapeutic agents that modulate protease activityin cells and tissues that express the protease. Experimental data asprovided in FIG. 1 indicates that protease proteins of the presentinvention are expressed in the liver, prostate, T cells from T cellleukemia, hepatocellular carcinoma, and lung tumor. Specifically, avirtual northern blot shows expression in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.

DESCRIPTION OF THE FIGURE SHEETS

[0039]FIG. 1 provides the nucleotide sequence of a cDNA molecule ortranscript sequence that encodes the protease protein of the presentinvention. (SEQ ID NO:1) In addition, structure and functionalinformation is provided, such as ATG start, stop and tissuedistribution, where available, that allows one to readily determinespecific uses of inventions based on this molecular sequence.Experimental data as provided in FIG. 1 indicates that protease proteinsof the present invention are expressed in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor.

[0040]FIG. 2 provides the predicted amino acid sequence of the proteaseof the present invention. (SEQ ID NO:2) In addition structure andfunctional information such as protein family, function, andmodification sites is provided where available, allowing one to readilydetermine specific uses of inventions based on this molecular sequence.

[0041]FIG. 3 provides genomic sequences that span the gene encoding theprotease protein of the present invention. (SEQ ID NO:3) In additionstructure and functional information, such as intron/exon structure,promoter location, etc., is provided where available, allowing one toreadily determine specific uses of inventions based on this molecularsequence. Twelve (12) SNPs, including 3 indels, have been identified inthe gene encoding the protease protein provided by the present inventionand are given in FIG. 3.

DETAILED DESCRIPTION OF THE INVENTION

[0042] General Description

[0043] The present invention is based on the sequencing of the humangenome. During the sequencing and assembly of the human genome, analysisof the sequence information revealed previously unidentified fragmentsof the human genome that encode peptides that share structural and/orsequence homology to protein/peptide/domains identified andcharacterized within the art as being a protease protein or part of aprotease protein and are related to the hepsin protease subfamily.Utilizing these sequences, additional genomic sequences were assembledand transcript and/or cDNA sequences were isolated and characterized.Based on this analysis, the present invention provides amino acidsequences of human protease peptides and proteins that are related tothe hepsin protease subfamily, nucleic acid sequences in the form oftranscript sequences, cDNA sequences and/or genomic sequences thatencode these protease peptides and proteins, nucleic acid variation(allelic information), tissue distribution of expression, andinformation about the closest art known protein/peptide/domain that hasstructural or sequence homology to the protease of the presentinvention.

[0044] In addition to being previously unknown, the peptides that areprovided in the present invention are selected based on their ability tobe used for the development of commercially important products andservices. Specifically, the present peptides are selected based onhomology and/or structural relatedness to known protease proteins of thehepsin protease subfamily and the expression pattern observed.Experimental data as provided in FIG. 1 indicates that protease proteinsof the present invention are expressed in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor. The art has clearly established the commercial importance ofmembers of this family of proteins and proteins that have expressionpatterns similar to that of the present gene. Some of the more specificfeatures of the peptides of the present invention, and the uses thereof,are described herein, particularly in the Background of the Inventionand in the annotation provided in the Figures, and/or are known withinthe art for each of the known hepsin family or subfamily of proteaseproteins.

[0045] Specific Embodiments

[0046] Peptide Molecules

[0047] The present invention provides nucleic acid sequences that encodeprotein molecules that have been identified as being members of theprotease family of proteins and are related to the hepsin proteasesubfamily (protein sequences are provided in FIG. 2, transcript/cDNAsequences are provided in FIG. 1 and genomic sequences are provided inFIG. 3). The peptide sequences provided in FIG. 2, as well as theobvious variants described herein, particularly allelic variants asidentified herein and using the information in FIG. 3, will be referredherein as the protease peptides of the present invention, proteasepeptides, or peptides/proteins of the present invention.

[0048] The present invention provides isolated peptide and proteinmolecules that consist of, consist essentially of, or comprise the aminoacid sequences of the protease peptides disclosed in the FIG. 2,(encoded by the nucleic acid molecule shown in FIG. 1, transcript/cDNAor FIG. 3, genomic sequence), as well as all obvious variants of thesepeptides that are within the art to make and use. Some of these variantsare described in detail below.

[0049] As used herein, a peptide is said to be “isolated” or “purified”when it is substantially free of cellular material or free of chemicalprecursors or other chemicals. The peptides of the present invention canbe purified to homogeneity or other degrees of purity. The level ofpurification will be based on the intended use. The critical feature isthat the preparation allows for the desired function of the peptide,even if in the presence of considerable amounts of other components (thefeatures of an isolated nucleic acid molecule is discussed below).

[0050] In some uses, “substantially free of cellular material” includespreparations of the peptide having less than about 30% (by dry weight)other proteins (i.e., contaminating protein), less than about 20% otherproteins, less than about 10% other proteins, or less than about 5%other proteins. When the peptide is recombinantly produced, it can alsobe substantially free of culture medium, i.e., culture medium representsless than about 20% of the volume of the protein preparation.

[0051] The language “substantially free of chemical precursors or otherchemicals” includes preparations of the peptide in which it is separatedfrom chemical precursors or other chemicals that are involved in itssynthesis. In one embodiment, the language “substantially free ofchemical precursors or other chemicals” includes preparations of theprotease peptide having less than about 30% (by dry weight) chemicalprecursors or other chemicals, less than about 20% chemical precursorsor other chemicals, less than about 10% chemical precursors or otherchemicals, or less than about 5% chemical precursors or other chemicals.

[0052] The isolated protease peptide can be purified from cells thatnaturally express it, purified from cells that have been altered toexpress it (recombinant), or synthesized using known protein synthesismethods. Experimental data as provided in FIG. 1 indicates that proteaseproteins of the present invention are expressed in the liver, prostate,T cells from T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor. For example, a nucleic acid molecule encoding the proteasepeptide is cloned into an expression vector, the expression vectorintroduced into a host cell and the protein expressed in the host cell.The protein can then be isolated from the cells by an appropriatepurification scheme using standard protein purification techniques. Manyof these techniques are described in detail below.

[0053] Accordingly, the present invention provides proteins that consistof the amino acid sequences provided in FIG. 2 (SEQ ID NO:2), forexample, proteins encoded by the transcript/cDNA nucleic acid sequencesshown in FIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG.3 (SEQ ID NO:3). The amino acid sequence of such a protein is providedin FIG. 2. A protein consists of an amino acid sequence when the aminoacid sequence is the final amino acid sequence of the protein.

[0054] The present invention further provides proteins that consistessentially of the amino acid sequences provided in FIG. 2 (SEQ IDNO:2), for example, proteins encoded by the transcript/cDNA nucleic acidsequences shown in FIG. 1 (SEQ ID NO:1) and the genomic sequencesprovided in FIG. 3 (SEQ ID NO:3). A protein consists essentially of anamino acid sequence when such an amino acid sequence is present withonly a few additional amino acid residues, for example from about 1 toabout 100 or so additional residues, typically from 1 to about 20additional residues in the final protein.

[0055] The present invention further provides proteins that comprise theamino acid sequences provided in FIG. 2 (SEQ ID NO:2), for example,proteins encoded by the transcript/cDNA nucleic acid sequences shown inFIG. 1 (SEQ ID NO:1) and the genomic sequences provided in FIG. 3 (SEQID NO:3). A protein comprises an amino acid sequence when the amino acidsequence is at least part of the final amino acid sequence of theprotein. In such a fashion, the protein can be only the peptide or haveadditional amino acid molecules, such as amino acid residues (contiguousencoded sequence) that are naturally associated with it or heterologousamino acid residues/peptide sequences. Such a protein can have a fewadditional amino acid residues or can comprise several hundred or moreadditional amino acids. The preferred classes of proteins that arecomprised of the protease peptides of the present invention are thenaturally occurring mature proteins. A brief description of how varioustypes of these proteins can be made/isolated is provided below.

[0056] The protease peptides of the present invention can be attached toheterologous sequences to form chimeric or fusion proteins. Suchchimeric and fusion proteins comprise a protease peptide operativelylinked to a heterologous protein having an amino acid sequence notsubstantially homologous to the protease peptide. “Operatively linked”indicates that the protease peptide and the heterologous protein arefused in-frame. The heterologous protein can be fused to the N-terminusor C-terminus of the protease peptide.

[0057] In some uses, the fusion protein does not affect the activity ofthe protease peptide per se. For example, the fusion protein caninclude, but is not limited to, enzymatic fusion proteins, for examplebeta-galactosidase fusions, yeast two-hybrid GAL fusions, poly-Hisfusions, MYC-tagged, HI-tagged and Ig fusions. Such fusion proteins,particularly poly-His fusions, can facilitate the purification ofrecombinant protease peptide. In certain host cells (e.g., mammalianhost cells), expression and/or secretion of a protein can be increasedby using a heterologous signal sequence.

[0058] A chimeric or fusion protein can be produced by standardrecombinant DNA techniques. For example, DNA fragments coding for thedifferent protein sequences are ligated together in-frame in accordancewith conventional techniques. In another embodiment, the fusion gene canbe synthesized by conventional techniques including automated DNAsynthesizers. Alternatively, PCR amplification of gene fragments can becarried out using anchor primers which give rise to complementaryoverhangs between two consecutive gene fragments which can subsequentlybe annealed and re-amplified to generate a chimeric gene sequence (seeAusubel et al., Current Protocols in Molecular Biology, 1992). Moreover,many expression vectors are commercially available that already encode afusion moiety (e.g., a GST protein). A protease peptide-encoding nucleicacid can be cloned into such an expression vector such that the fusionmoiety is linked in-frame to the protease peptide.

[0059] As mentioned above, the present invention also provides andenables obvious variants of the amino acid sequence of the proteins ofthe present invention, such as naturally occurring mature forms of thepeptide, allelic/sequence variants of the peptides, non-naturallyoccurring recombinantly derived variants of the peptides, and orthologsand paralogs of the peptides. Such variants can readily be generatedusing art-known techniques in the fields of recombinant nucleic acidtechnology and protein biochemistry. It is understood, however, thatvariants exclude any amino acid sequences disclosed prior to theinvention.

[0060] Such variants can readily be identified/made using moleculartechniques and the sequence information disclosed herein. Further, suchvariants can readily be distinguished from other peptides based onsequence and/or structural homology to the protease peptides of thepresent invention. The degree of homology/identity present will be basedprimarily on whether the peptide is a functional variant ornon-functional variant, the amount of divergence present in the paralogfamily and the evolutionary distance between the orthologs.

[0061] To determine the percent identity of two amino acid sequences ortwo nucleic acid sequences, the sequences are aligned for optimalcomparison purposes (e.g., gaps can be introduced in one or both of afirst and a second amino acid or nucleic acid sequence for optimalalignment and non-homologous sequences can be disregarded for comparisonpurposes). In a preferred embodiment, at least 30%, 40%, 50%, 60%, 70%,80%, or 90% or more of the length of a reference sequence is aligned forcomparison purposes. The amino acid residues or nucleotides atcorresponding amino acid positions or nucleotide positions are thencompared. When a position in the first sequence is occupied by the sameamino acid residue or nucleotide as the corresponding position in thesecond sequence, then the molecules are identical at that position (asused herein amino acid or nucleic acid “identity” is equivalent to aminoacid or nucleic acid “homology”). The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which need to be introduced for optimal alignment of the twosequences.

[0062] The comparison of sequences and determination of percent identityand similarity between two sequences can be accomplished using amathematical algorithm. (Computational Molecular Biology, Lesk, A. M.,ed., Oxford University Press, New York, 1988; Biocomputing: Informaticsand Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Computer Analysis of sequence Data, Part 1, Griffin, A. M., and Griffin,H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis inMolecular Biology, von Heinje, G., Academic Press, 1987; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991). In a preferred embodiment, the percent identity betweentwo amino acid sequences is determined using the Needleman and Wunsch(J. Mol. Biol. (48):444-453 (1970)) algorithm which has beenincorporated into the GAP program in the GCG software package (availableat http://www.gcg.com), using either a Blossom 62 matrix or a PAM250matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a lengthweight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, thepercent identity between two nucleotide sequences is determined usingthe GAP program in the GCG software package (Devereux, J., et al.,Nucleic Acids Res. 12(1):387 (1984)) (available at http://www.gcg.com),using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, thepercent identity between two amino acid or nucleotide sequences isdetermined using the algorithm of E. Myers and W. Miller (CABIOS,4:11-17 (1989)) which has been incorporated into the ALIGN program(version 2.0), using a PAM120 weight residue table, a gap length penaltyof 12 and a gap penalty of 4.

[0063] The nucleic acid and protein sequences of the present inventioncan further be used as a “query sequence” to perform a search againstsequence databases to, for example, identify other family members orrelated sequences. Such searches can be performed using the NBLAST andXBLAST programs (version 2.0) of Altschul, et al. (J. Mol. Biol.215:403-10 (1990)). BLAST nucleotide searches can be performed with theNBLAST program, score=100, wordlength=12 to obtain nucleotide sequenceshomologous to the nucleic acid molecules of the invention. BLAST proteinsearches can be performed with the XBLAST program, score=50,wordlength=3 to obtain amino acid sequences homologous to the proteinsof the invention. To obtain gapped alignments for comparison purposes,Gapped BLAST can be utilized as described in Altschul et al. (NucleicAcids Res. 25(17):3389-3402 (1997)). When utilizing BLAST and gappedBLAST programs, the default parameters of the respective programs (e.g.,XBLAST and NBLAST) can be used.

[0064] Full-length pre-processed forms, as well as mature processedforms, of proteins that comprise one of the peptides of the presentinvention can readily be identified as having complete sequence identityto one of the protease peptides of the present invention as well asbeing encoded by the same genetic locus as the protease peptide providedherein. As indicated by the data presented in FIG. 3, the map positionwas determined to be on chromosome 19 by ePCR, and confirmed withradiation hybrid mapping.

[0065] Allelic variants of a protease peptide can readily be identifiedas being a human protein having a high degree (significant) of sequencehomology/identity to at least a portion of the protease peptide as wellas being encoded by the same genetic locus as the protease peptideprovided herein. Genetic locus can readily be determined based on thegenomic information provided in FIG. 3, such as the genomic sequencemapped to the reference human. As indicated by the data presented inFIG. 3, the map position was determined to be on chromosome 19 by ePCR,and confirmed with radiation hybrid mapping. As used herein, twoproteins (or a region of the proteins) have significant homology whenthe amino acid sequences are typically at least about 70-80%, 80-90%,and more typically at least about 90-95% or more homologous. Asignificantly homologous amino acid sequence, according to the presentinvention, will be encoded by a nucleic acid sequence that willhybridize to a protease peptide encoding nucleic acid molecule understringent conditions as more fully described below.

[0066]FIG. 3 provides information on SNPs that have been identified in agene encoding the protease protein of the present invention. Twelve (12)SNP variants were found, including 3 indels (indicated by a “-”) and 1SNP in exons, none of which cause changes in the amino acid sequence.

[0067] Paralogs of a protease peptide can readily be identified ashaving some degree of significant sequence homology/identity to at leasta portion of the protease peptide, as being encoded by a gene fromhumans, and as having similar activity or function. Two proteins willtypically be considered paralogs when the amino acid sequences aretypically at least about 60% or greater, and more typically at leastabout 70% or greater homology through a given region or domain. Suchparalogs will be encoded by a nucleic acid sequence that will hybridizeto a protease peptide encoding nucleic acid molecule under moderate tostringent conditions as more fully described below.

[0068] Orthologs of a protease peptide can readily be identified ashaving some degree of significant sequence homology/identity to at leasta portion of the protease peptide as well as being encoded by a genefrom another organism. Preferred orthologs will be isolated frommammals, preferably primates, for the development of human therapeutictargets and agents. Such orthologs will be encoded by a nucleic acidsequence that will hybridize to a protease peptide encoding nucleic acidmolecule under moderate to stringent conditions, as more fully describedbelow, depending on the degree of relatedness of the two organismsyielding the proteins. As indicated by the data presented in FIG. 3, themap position was determined to be on chromosome 19 by ePCR, andconfirmed with radiation hybrid mapping.

[0069]FIG. 3 provides information on SNPs that have been identified in agene encoding the protease protein of the present invention. Twelve (12)SNP variants were found, including 3 indels (indicated by a “-”) and 1SNP in exons, none of which cause changes in the amino acid sequence.

[0070] Non-naturally occurring variants of the protease peptides of thepresent invention can readily be generated using recombinant techniques.Such variants include, but are not limited to deletions, additions andsubstitutions in the amino acid sequence of the protease peptide. Forexample, one class of substitutions are conserved amino acidsubstitution. Such substitutions are those that substitute a given aminoacid in a protease peptide by another amino acid of likecharacteristics. Typically seen as conservative substitutions are thereplacements, one for another, among the aliphatic amino acids Ala, Val,Leu, and Ile; interchange of the hydroxyl residues Ser and Thr; exchangeof the acidic residues Asp and Glu; substitution between the amideresidues Asn and Gln; exchange of the basic residues Lys and Arg; andreplacements among the aromatic residues Phe and Tyr. Guidanceconcerning which amino acid changes are likely to be phenotypicallysilent are found in Bowie et al., Science 247:1306-1310 (1990).

[0071] Variant protease peptides can be fully functional or can lackfunction in one or more activities, e.g. ability to bind substrate,ability to cleave substrate, ability to participate in a signalingpathway, etc. Fully functional variants typically contain onlyconservative variation or variation in non-critical residues or innon-critical regions. FIG. 2 provides the result of protein analysis andcan be used to identify critical domains/regions. Functional variantscan also contain substitution of similar amino acids that result in nochange or an insignificant change in function. Alternatively, suchsubstitutions may positively or negatively affect function to somedegree.

[0072] Non-functional variants typically contain one or morenon-conservative amino acid substitutions, deletions, insertions,inversions, or truncation or a substitution, insertion, inversion, ordeletion in a critical residue or critical region.

[0073] Amino acids that are essential for function can be identified bymethods known in the art, such as site-directed mutagenesis oralanine-scanning mutagenesis (Cunningham et al., Science 244:1081-1085(1989)), particularly using the results provided in FIG. 2. The latterprocedure introduces single alanine mutations at every residue in themolecule. The resulting mutant molecules are then tested for biologicalactivity such as protease activity or in assays such as an in vitroproliferative activity. Sites that are critical for bindingpartner/substrate binding can also be determined by structural analysissuch as crystallization, nuclear magnetic resonance or photoaffinitylabeling (Smith et al., J. Mol. Biol. 224:899-904 (1992); de Vos et al.Science 255:306-312 (1992)).

[0074] The present invention further provides fragments of the proteasepeptides, in addition to proteins and peptides that comprise and consistof such fragments, particularly those comprising the residues identifiedin FIG. 2. The fragments to which the invention pertains, however, arenot to be construed as encompassing fragments that may be disclosedpublicly prior to the present invention.

[0075] As used herein, a fragment comprises at least 8, 10, 12, 14, 16,or more contiguous amino acid residues from a protease peptide. Suchfragments can be chosen based on the ability to retain one or more ofthe biological activities of the protease peptide or could be chosen forthe ability to perform a function, e.g. bind a substrate or act as animmunogen. Particularly important fragments are biologically activefragments, peptides that are, for example, about 8 or more amino acidsin length. Such fragments will typically comprise a domain or motif ofthe protease peptide, e.g., active site, a transmembrane domain or asubstrate-binding domain. Further, possible fragments include, but arenot limited to, domain or motif containing fragments, soluble peptidefragments, and fragments containing immunogenic structures. Predicteddomains and functional sites are readily identifiable by computerprograms well known and readily available to those of skill in the art(e.g., PROSITE analysis). The results of one such analysis are providedin FIG. 2.

[0076] Polypeptides often contain amino acids other than the 20 aminoacids commonly referred to as the 20 naturally occurring amino acids.Further, many amino acids, including the terminal amino acids, may bemodified by natural processes, such as processing and otherpost-translational modifications, or by chemical modification techniqueswell known in the art. Common modifications that occur naturally inprotease peptides are described in basic texts, detailed monographs, andthe research literature, and they are well known to those of skill inthe art (some of these features are identified in FIG. 2).

[0077] Known modifications include, but are not limited to, acetylation,acylation, ADP-ribosylation, amidation, covalent attachment of flavin,covalent attachment of a heme moiety, covalent attachment of anucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, demethylation,formation of covalent crosslinks, formation of cystine, formation ofpyroglutamate, formylation, gamma carboxylation, glycosylation, GPIanchor formation, hydroxylation, iodination, methylation,myristoylation, oxidation, proteolytic processing, phosphorylation,prenylation, racemization, selenoylation, sulfation, transfer-RNAmediated addition of amino acids to proteins such as arginylation, andubiquitination.

[0078] Such modifications are well known to those of skill in the artand have been described in great detail in the scientific literature.Several particularly common modifications, glycosylation, lipidattachment, sulfation, gamma-carboxylation of glutamic acid residues,hydroxylation and ADP-ribosylation, for instance, are described in mostbasic texts, such as Proteins—Structure and Molecular Properties, 2ndEd., T. E. Creighton, W. H. Freeman and Company, New York (1993). Manydetailed reviews are available on this subject, such as by Wold, F.,Posttranslational Covalent Modification of Proteins, B. C. Johnson, Ed.,Academic Press, New York 1-12 (1983); Seifter et al. (Meth. Enzymol.182: 626-646 (1990)) and Rattan et al. (Ann. N.Y. Acad. Sci. 663:48-62(1992)).

[0079] Accordingly, the protease peptides of the present invention alsoencompass derivatives or analogs in which a substituted amino acidresidue is not one encoded by the genetic code, in which a substituentgroup is included, in which the mature protease peptide is fused withanother compound, such as a compound to increase the half-life of theprotease peptide (for example, polyethylene glycol), or in which theadditional amino acids are fused to the mature protease peptide, such asa leader or secretory sequence or a sequence for purification of themature protease peptide or a pro-protein sequence.

[0080] Protein/Peptide Uses

[0081] The proteins of the present invention can be used in substantialand specific assays related to the functional information provided inthe Figures; to raise antibodies or to elicit another immune response;as a reagent (including the labeled reagent) in assays designed toquantitatively determine levels of the protein (or its binding partneror ligand) in biological fluids; and as markers for tissues in which thecorresponding protein is preferentially expressed (either constitutivelyor at a particular stage of tissue differentiation or development or ina disease state). Where the protein binds or potentially binds toanother protein or ligand (such as, for example, in a protease-effectorprotein interaction or protease-ligand interaction), the protein can beused to identify the binding partner/ligand so as to develop a system toidentify inhibitors of the binding interaction. Any or all of these usesare capable of being developed into reagent grade or kit format forcommercialization as commercial products.

[0082] Methods for performing the uses listed above are well known tothose skilled in the art. References disclosing such methods include“Molecular Cloning: A Laboratory Manual”, 2d ed., Cold Spring HarborLaboratory Press, Sambrook, J., E. F. Fritsch and T. Maniatis eds.,1989, and “Methods in Enzymology: Guide to Molecular CloningTechniques”, Academic Press, Berger, S. L. and A. R. Kimmel eds., 1987.

[0083] Substantial chemical and structural homology exists between thehepsin protein described herein and cell surface serine proteases (seeFIG. 1). As discussed in the background, cell surface serine proteasesare known in the art to be involved in tumor growth and consequently mayplay a role in cancers such as ovarian cancer. For more information, seeTanimoto, et al., Cancer Res. Jul. 15, 1997;57(14):2884-7. Accordingly,the hepsin protein, and the encoding gene, provided by the presentinvention is useful for treating, preventing, and/or diagnosing cancerssuch as ovarian cancer.

[0084] The potential uses of the peptides of the present invention arebased primarily on the source of the protein as well as the class/actionof the protein. For example, proteases isolated from humans and theirhuman/mammalian orthologs serve as targets for identifying agents foruse in mammalian therapeutic applications, e.g. a human drug,particularly in modulating a biological or pathological response in acell or tissue that expresses the protease. Experimental data asprovided in FIG. 1 indicates that protease proteins of the presentinvention are expressed in the liver, prostate, T cells from T cellleukemia, hepatocellular carcinoma, and lung tumor. Specifically, avirtual northern blot shows expression in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor. A largepercentage of pharmaceutical agents are being developed that modulatethe activity of protease proteins, particularly members of the hepsinsubfamily (see Background of the Invention). The structural andfunctional information provided in the Background and Figures providespecific and substantial uses for the molecules of the presentinvention, particularly in combination with the expression informationprovided in FIG. 1. Experimental data as provided in FIG. 1 indicatesthat protease proteins of the present invention are expressed in theliver, prostate, T cells from T cell leukemia, hepatocellular carcinoma,and lung tumor. Specifically, a virtual northern blot shows expressionin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Such uses can readily be determined using theinformation provided herein, that which is known in the art, and routineexperimentation.

[0085] The proteins of the present invention (including variants andfragments that may have been disclosed prior to the present invention)are useful for biological assays related to proteases that are relatedto members of the hepsin subfamily. Such assays involve any of the knownprotease functions or activities or properties useful for diagnosis andtreatment of protease-related conditions that are specific for thesubfamily of proteases that the one of the present invention belongs to,particularly in cells and tissues that express the protease.Experimental data as provided in FIG. 1 indicates that protease proteinsof the present invention are expressed in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor.

[0086] The proteins of the present invention are also useful in drugscreening assays, in cell-based or cell-free systems. Cell-based systemscan be native, i.e., cells that normally express the protease, as abiopsy or expanded in cell culture. Experimental data as provided inFIG. 1 indicates that protease proteins of the present invention areexpressed in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. Specifically, a virtualnorthern blot shows expression in the liver, prostate, T cells from Tcell leukemia, hepatocellular carcinoma, and lung tumor. In an alternateembodiment, cell-based assays involve recombinant host cells expressingthe protease protein.

[0087] The polypeptides can be used to identify compounds that modulateprotease activity of the protein in its natural state or an altered formthat causes a specific disease or pathology associated with theprotease. Both the proteases of the present invention and appropriatevariants and fragments can be used in high-throughput screens to assaycandidate compounds for the ability to bind to the protease. Thesecompounds can be further screened against a functional protease todetermine the effect of the compound on the protease activity. Further,these compounds can be tested in animal or invertebrate systems todetermine activity/effectiveness. Compounds can be identified thatactivate (agonist) or inactivate (antagonist) the protease to a desireddegree.

[0088] Further, the proteins of the present invention can be used toscreen a compound for the ability to stimulate or inhibit interactionbetween the protease protein and a molecule that normally interacts withthe protease protein, e.g. a substrate or a component of the signalpathway that the protease protein normally interacts (for example, aprotease). Such assays typically include the steps of combining theprotease protein with a candidate compound under conditions that allowthe protease protein, or fragment, to interact with the target molecule,and to detect the formation of a complex between the protein and thetarget or to detect the biochemical consequence of the interaction withthe protease protein and the target, such as any of the associatedeffects of signal transduction such as protein cleavage, cAMP turnover,and adenylate cyclase activation, etc.

[0089] Candidate compounds include, for example, 1) peptides such assoluble peptides, including Ig-tailed fusion peptides and members ofrandom peptide libraries (see, e.g., Lam et al., Nature 354:82-84(1991); Houghten et al., Nature 354:84-86 (1991)) and combinatorialchemistry-derived molecular libraries made of D- and/or L-configurationamino acids; 2) phosphopeptides (e.g., members of random and partiallydegenerate, directed phosphopeptide libraries, see, e.g., Songyang etal., Cell 72:767-778 (1993)); 3) antibodies (e.g., polyclonal,monoclonal, humanized, anti-idiotypic, chimeric, and single chainantibodies as well as Fab, F(ab′)₂, Fab expression library fragments,and epitope-binding fragments of antibodies); and 4) small organic andinorganic molecules (e.g., molecules obtained from combinatorial andnatural product libraries).

[0090] One candidate compound is a soluble fragment of the receptor thatcompetes for substrate binding. Other candidate compounds include mutantproteases or appropriate fragments containing mutations that affectprotease function and thus compete for substrate. Accordingly, afragment that competes for substrate, for example with a higheraffinity, or a fragment that binds substrate but does not allow release,is encompassed by the invention.

[0091] The invention further includes other end point assays to identifycompounds that modulate (stimulate or inhibit) protease activity. Theassays typically involve an assay of events in the signal transductionpathway that indicate protease activity. Thus, the cleavage of asubstrate, inactivation/activation of a protein, a change in theexpression of genes that are up- or down-regulated in response to theprotease protein dependent signal cascade can be assayed.

[0092] Any of the biological or biochemical functions mediated by theprotease can be used as an endpoint assay. These include all of thebiochemical or biochemical/biological events described herein, in thereferences cited herein, incorporated by reference for these endpointassay targets, and other functions known to those of ordinary skill inthe art or that can be readily identified using the information providedin the Figures, particularly FIG. 2. Specifically, a biological functionof a cell or tissues that expresses the protease can be assayed.Experimental data as provided in FIG. 1 indicates that protease proteinsof the present invention are expressed in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor.

[0093] Binding and/or activating compounds can also be screened by usingchimeric protease proteins in which the amino terminal extracellulardomain, or parts thereof, the entire transmembrane domain or subregions,such as any of the seven transmembrane segments or any of theintracellular or extracellular loops and the carboxy terminalintracellular domain, or parts thereof, can be replaced by heterologousdomains or subregions. For example, a substrate-binding region can beused that interacts with a different substrate then that which isrecognized by the native protease. Accordingly, a different set ofsignal transduction components is available as an end-point assay foractivation. This allows for assays to be performed in other than thespecific host cell from which the protease is derived.

[0094] The proteins of the present invention are also useful incompetition binding assays in methods designed to discover compoundsthat interact with the protease (e.g. binding partners and/or ligands).Thus, a compound is exposed to a protease polypeptide under conditionsthat allow the compound to bind or to otherwise interact with thepolypeptide. Soluble protease polypeptide is also added to the mixture.If the test compound interacts with the soluble protease polypeptide, itdecreases the amount of complex formed or activity from the proteasetarget. This type of assay is particularly useful in cases in whichcompounds are sought that interact with specific regions of theprotease. Thus, the soluble polypeptide that competes with the targetprotease region is designed to contain peptide sequences correspondingto the region of interest.

[0095] To perform cell free drug screening assays, it is sometimesdesirable to immobilize either the protease protein, or fragment, or itstarget molecule to facilitate separation of complexes from uncomplexedforms of one or both of the proteins, as well as to accommodateautomation of the assay.

[0096] Techniques for immobilizing proteins on matrices can be used inthe drug screening assays. In one embodiment, a fusion protein can beprovided which adds a domain that allows the protein to be bound to amatrix. For example, glutathione-S-transferase fusion proteins can beadsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis,Mo.) or glutathione derivatized microtitre plates, which are thencombined with the cell lysates (e.g., ³⁵S-labeled) and the candidatecompound, and the mixture incubated under conditions conducive tocomplex formation (e.g., at physiological conditions for salt and pH).Following incubation, the beads are washed to remove any unbound label,and the matrix immobilized and radiolabel determined directly, or in thesupernatant after the complexes are dissociated. Alternatively, thecomplexes can be dissociated from the matrix, separated by SDS-PAGE, andthe level of protease-binding protein found in the bead fractionquantitated from the gel using standard electrophoretic techniques. Forexample, either the polypeptide or its target molecule can beimmobilized utilizing conjugation of biotin and streptavidin usingtechniques well known in the art. Alternatively, antibodies reactivewith the protein but which do not interfere with binding of the proteinto its target molecule can be derivatized to the wells of the plate, andthe protein trapped in the wells by antibody conjugation. Preparationsof a protease-binding protein and a candidate compound are incubated inthe protease protein-presenting wells and the amount of complex trappedin the well can be quantitated. Methods for detecting such complexes, inaddition to those described above for the GST-immobilized complexes,include immunodetection of complexes using antibodies reactive with theprotease protein target molecule, or which are reactive with proteaseprotein and compete with the target molecule, as well as enzyme-linkedassays which rely on detecting an enzymatic activity associated with thetarget molecule.

[0097] Agents that modulate one of the proteases of the presentinvention can be identified using one or more of the above assays, aloneor in combination. It is generally preferable to use a cell-based orcell free system first and then confirm activity in an animal or othermodel system. Such model systems are well known in the art and canreadily be employed in this context.

[0098] Modulators of protease protein activity identified according tothese drug screening assays can be used to treat a subject with adisorder mediated by the protease pathway, by treating cells or tissuesthat express the protease. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. These methods of treatmentinclude the steps of administering a modulator of protease activity in apharmaceutical composition to a subject in need of such treatment, themodulator being identified as described herein. In yet another aspect ofthe invention, the protease proteins can be used as “bait proteins” in atwo-hybrid assay or three-hybrid assay (see, e.g., U.S. Pat. No.5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J.Biol. Chem. 268:12046-12054; Bartel et al. (1993) Biotechniques14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and BrentWO94/10300), to identify other proteins, which bind to or interact withthe protease and are involved in protease activity. Suchprotease-binding proteins are also likely to be involved in thepropagation of signals by the protease proteins or protease targets as,for example, downstream elements of a protease-mediated signalingpathway. Alternatively, such protease-binding proteins are likely to beprotease inhibitors.

[0099] The two-hybrid system is based on the modular nature of mosttranscription factors, which consist of separable DNA-binding andactivation domains. Briefly, the assay utilizes two different DNAconstructs. In one construct, the gene that codes for a protease proteinis fused to a gene encoding the DNA binding domain of a knowntranscription factor (e.g., GAL-4). In the other construct, a DNAsequence, from a library of DNA sequences, that encodes an unidentifiedprotein (“prey” or “sample”) is fused to a gene that codes for theactivation domain of the known transcription factor. If the “bait” andthe “prey” proteins are able to interact, in vivo, forming aprotease-dependent complex, the DNA-binding and activation domains ofthe transcription factor are brought into close proximity. Thisproximity allows transcription of a reporter gene (e.g., LacZ) which isoperably linked to a transcriptional regulatory site responsive to thetranscription factor. Expression of the reporter gene can be detectedand cell colonies containing the functional transcription factor can beisolated and used to obtain the cloned gene which encodes the proteinwhich interacts with the protease protein.

[0100] This invention further pertains to novel agents identified by theabove-described screening assays. Accordingly, it is within the scope ofthis invention to further use an agent identified as described herein inan appropriate animal model. For example, an agent identified asdescribed herein (e.g., a protease-modulating agent, an antisenseprotease nucleic acid molecule, a protease-specific antibody, or aprotease-binding partner) can be used in an animal or other model todetermine the efficacy, toxicity, or side effects of treatment with suchan agent. Alternatively, an agent identified as described herein can beused in an animal or other model to determine the mechanism of action ofsuch an agent. Furthermore, this invention pertains to uses of novelagents identified by the above-described screening assays for treatmentsas described herein.

[0101] The protease proteins of the present invention are also useful toprovide a target for diagnosing a disease or predisposition to diseasemediated by the peptide. Accordingly, the invention provides methods fordetecting the presence, or levels of, the protein (or encoding mRNA) ina cell, tissue, or organism. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. The method involves contactinga biological sample with a compound capable of interacting with theprotease protein such that the interaction can be detected. Such anassay can be provided in a single detection format or a multi-detectionformat such as an antibody chip array.

[0102] One agent for detecting a protein in a sample is an antibodycapable of selectively binding to protein. A biological sample includestissues, cells and biological fluids isolated from a subject, as well astissues, cells and fluids present within a subject.

[0103] The peptides of the present invention also provide targets fordiagnosing active protein activity, disease, or predisposition todisease, in a patient having a variant peptide, particularly activitiesand conditions that are known for other members of the family ofproteins to which the present one belongs. Thus, the peptide can beisolated from a biological sample and assayed for the presence of agenetic mutation that results in aberrant peptide. This includes aminoacid substitution, deletion, insertion, rearrangement, (as the result ofaberrant splicing events), and inappropriate post-translationalmodification. Analytic methods include altered electrophoretic mobility,altered tryptic peptide digest, altered protease activity in cell-basedor cell-free assay, alteration in substrate or antibody-binding pattern,altered isoelectric point, direct amino acid sequencing, and any otherof the known assay techniques useful for detecting mutations in aprotein. Such an assay can be provided in a single detection format or amulti-detection format such as an antibody chip array.

[0104] In vitro techniques for detection of peptide include enzymelinked immunosorbent assays (ELISAs), Western blots,immunoprecipitations and immunofluorescence using a detection reagent,such as an antibody or protein binding agent. Alternatively, the peptidecan be detected in vivo in a subject by introducing into the subject alabeled anti-peptide antibody or other types of detection agent. Forexample, the antibody can be labeled with a radioactive marker whosepresence and location in a subject can be detected by standard imagingtechniques. Particularly useful are methods that detect the allelicvariant of a peptide expressed in a subject and methods which detectfragments of a peptide in a sample.

[0105] The peptides are also useful in pharmacogenomic analysis.Pharmacogenomics deal with clinically significant hereditary variationsin the response to drugs due to altered drug disposition and abnormalaction in affected persons. See, e.g., Eichelbaum, M. (Clin. Exp.Pharmacol. Physiol. 23(10-11):983-985 (1996)), and Linder, M. W. (Clin.Chem. 43(2):254-266 (1997)). The clinical outcomes of these variationsresult in severe toxicity of therapeutic drugs in certain individuals ortherapeutic failure of drugs in certain individuals as a result ofindividual variation in metabolism. Thus, the genotype of the individualcan determine the way a therapeutic compound acts on the body or the waythe body metabolizes the compound. Further, the activity of drugmetabolizing enzymes effects both the intensity and duration of drugaction. Thus, the pharmacogenomics of the individual permit theselection of effective compounds and effective dosages of such compoundsfor prophylactic or therapeutic treatment based on the individual'sgenotype. The discovery of genetic polymorphisms in some drugmetabolizing enzymes has explained why some patients do not obtain theexpected drug effects, show an exaggerated drug effect, or experienceserious toxicity from standard drug dosages. Polymorphisms can beexpressed in the phenotype of the extensive metabolizer and thephenotype of the poor metabolizer. Accordingly, genetic polymorphism maylead to allelic protein variants of the protease protein in which one ormore of the protease functions in one population is different from thosein another population. The peptides thus allow a target to ascertain agenetic predisposition that can affect treatment modality. Thus, in aligand-based treatment, polymorphism may give rise to amino terminalextracellular domains and/or other substrate-binding regions that aremore or less active in substrate binding, and protease activation.Accordingly, substrate dosage would necessarily be modified to maximizethe therapeutic effect within a given population containing apolymorphism. As an alternative to genotyping, specific polymorphicpeptides could be identified.

[0106] The peptides are also useful for treating a disordercharacterized by an absence of, inappropriate, or unwanted expression ofthe protein. Experimental data as provided in FIG. 1 indicates thatprotease proteins of the present invention are expressed in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor. Specifically, a virtual northern blot shows expression inthe liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Accordingly, methods for treatment includethe use of the protease protein or fragments.

[0107] Antibodies

[0108] The invention also provides antibodies that selectively bind toone of the peptides of the present invention, a protein comprising sucha peptide, as well as variants and fragments thereof. As used herein, anantibody selectively binds a target peptide when it binds the targetpeptide and does not significantly bind to unrelated proteins. Anantibody is still considered to selectively bind a peptide even if italso binds to other proteins that are not substantially homologous withthe target peptide so long as such proteins share homology with afragment or domain of the peptide target of the antibody. In this case,it would be understood that antibody binding to the peptide is stillselective despite some degree of cross-reactivity.

[0109] As used herein, an antibody is defined in terms consistent withthat recognized within the art: they are multi-subunit proteins producedby a mammalian organism in response to an antigen challenge. Theantibodies of the present invention include polyclonal antibodies andmonoclonal antibodies, as well as fragments of such antibodies,including, but not limited to, Fab or F(ab′)₂, and Fv fragments.

[0110] Many methods are known for generating and/or identifyingantibodies to a given target peptide. Several such methods are describedby Harlow, Antibodies, Cold Spring Harbor Press, (1989).

[0111] In general, to generate antibodies, an isolated peptide is usedas an immunogen and is administered to a mammalian organism, such as arat, rabbit or mouse. The full-length protein, an antigenic peptidefragment or a fusion protein can be used. Particularly importantfragments are those covering functional domains, such as the domainsidentified in FIG. 2, and domain of sequence homology or divergenceamongst the family, such as those that can readily be identified usingprotein alignment methods and as presented in the Figures.

[0112] Antibodies are preferably prepared from regions or discretefragments of the protease proteins. Antibodies can be prepared from anyregion of the peptide as described herein. However, preferred regionswill include those involved in function/activity and/or protease/bindingpartner interaction. FIG. 2 can be used to identify particularlyimportant regions while sequence alignment can be used to identifyconserved and unique sequence fragments.

[0113] An antigenic fragment will typically comprise at least 8contiguous amino acid residues. The antigenic peptide can comprise,however, at least 10, 12, 14, 16 or more amino acid residues. Suchfragments can be selected on a physical property, such as fragmentscorrespond to regions that are located on the surface of the protein,e.g., hydrophilic regions or can be selected based on sequenceuniqueness (see FIG. 2).

[0114] Detection on an antibody of the present invention can befacilitated by coupling (i.e., physically linking) the antibody to adetectable substance. Examples of detectable substances include variousenzymes, prosthetic groups, fluorescent materials, luminescentmaterials, bioluminescent materials, and radioactive materials. Examplesof suitable enzymes include horseradish peroxidase, alkalinephosphatase, β-galactosidase, or acetylcholinesterase; examples ofsuitable prosthetic group complexes include streptavidin/biotin andavidin/biotin; examples of suitable fluorescent materials includeumbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine,dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; anexample of a luminescent material includes luminol; examples ofbioluminescent materials include luciferase, luciferin, and aequorin,and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or³H.

[0115] Antibody Uses

[0116] The antibodies can be used to isolate one of the proteins of thepresent invention by standard techniques, such as affinitychromatography or immunoprecipitation. The antibodies can facilitate thepurification of the natural protein from cells and recombinantlyproduced protein expressed in host cells. In addition, such antibodiesare useful to detect the presence of one of the proteins of the presentinvention in cells or tissues to determine the pattern of expression ofthe protein among various tissues in an organism and over the course ofnormal development. Experimental data as provided in FIG. 1 indicatesthat protease proteins of the present invention are expressed in theliver, prostate, T cells from T cell leukemia, hepatocellular carcinoma,and lung tumor. Specifically, a virtual northern blot shows expressionin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Further, such antibodies can be used todetect protein in situ, in vitro, or in a cell lysate or supernatant inorder to evaluate the abundance and pattern of expression. Also, suchantibodies can be used to assess abnormal tissue distribution orabnormal expression during development or progression of a biologicalcondition. Antibody detection of circulating fragments of the fulllength protein can be used to identify turnover.

[0117] Further, the antibodies can be used to assess expression indisease states such as in active stages of the disease or in anindividual with a predisposition toward disease related to the protein'sfunction. When a disorder is caused by an inappropriate tissuedistribution, developmental expression, level of expression of theprotein, or expressed/processed form, the antibody can be preparedagainst the normal protein. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. If a disorder is characterizedby a specific mutation in the protein, antibodies specific for thismutant protein can be used to assay for the presence of the specificmutant protein.

[0118] The antibodies can also be used to assess normal and aberrantsubcellular localization of cells in the various tissues in an organism.Experimental data as provided in FIG. 1 indicates that protease proteinsof the present invention are expressed in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Specifically, a virtual northern blot shows expression in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor. The diagnostic uses can be applied, not only in genetictesting, but also in monitoring a treatment modality. Accordingly, wheretreatment is ultimately aimed at correcting expression level or thepresence of aberrant sequence and aberrant tissue distribution ordevelopmental expression, antibodies directed against the protein orrelevant fragments can be used to monitor therapeutic efficacy.

[0119] Additionally, antibodies are useful in pharmacogenomic analysis.Thus, antibodies prepared against polymorphic proteins can be used toidentify individuals that require modified treatment modalities. Theantibodies are also useful as diagnostic tools as an immunologicalmarker for aberrant protein analyzed by electrophoretic mobility,isoelectric point, tryptic peptide digest, and other physical assaysknown to those in the art.

[0120] The antibodies are also useful for tissue typing. Experimentaldata as provided in FIG. 1 indicates that protease proteins of thepresent invention are expressed in the liver, prostate, T cells from Tcell leukemia, hepatocellular carcinoma, and lung tumor. Specifically, avirtual northern blot shows expression in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor. Thus,where a specific protein has been correlated with expression in aspecific tissue, antibodies that are specific for this protein can beused to identify a tissue type.

[0121] The antibodies are also useful for inhibiting protein function,for example, blocking the binding of the protease peptide to a bindingpartner such as a substrate. These uses can also be applied in atherapeutic context in which treatment involves inhibiting the protein'sfunction. An antibody can be used, for example, to block binding, thusmodulating (agonizing or antagonizing) the peptides activity. Antibodiescan be prepared against specific fragments containing sites required forfunction or against intact protein that is associated with a cell orcell membrane. See FIG. 2 for structural information relating to theproteins of the present invention.

[0122] The invention also encompasses kits for using antibodies todetect the presence of a protein in a biological sample. The kit cancomprise antibodies such as a labeled or labelable antibody and acompound or agent for detecting protein in a biological sample; meansfor determining the amount of protein in the sample; means for comparingthe amount of protein in the sample with a standard; and instructionsfor use. Such a kit can be supplied to detect a single protein orepitope or can be configured to detect one of a multitude of epitopes,such as in an antibody detection array. Arrays are described in detailbelow for nucleic acid arrays and similar methods have been developedfor antibody arrays.

[0123] Nucleic Acid Molecules

[0124] The present invention further provides isolated nucleic acidmolecules that encode a protease peptide or protein of the presentinvention (cDNA, transcript and genomic sequence). Such nucleic acidmolecules will consist of, consist essentially of, or comprise anucleotide sequence that encodes one of the protease peptides of thepresent invention, an allelic variant thereof, or an ortholog or paralogthereof.

[0125] As used herein, an “isolated” nucleic acid molecule is one thatis separated from other nucleic acid present in the natural source ofthe nucleic acid. Preferably, an “isolated” nucleic acid is free ofsequences which naturally flank the nucleic acid (i.e., sequenceslocated at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA ofthe organism from which the nucleic acid is derived. However, there canbe some flanking nucleotide sequences, for example up to about 5 KB, 4KB, 3 KB, 2 KB, or 1 KB or less, particularly contiguous peptideencoding sequences and peptide encoding sequences within the same genebut separated by introns in the genomic sequence. The important point isthat the nucleic acid is isolated from remote and unimportant flankingsequences such that it can be subjected to the specific manipulationsdescribed herein such as recombinant expression, preparation of probesand primers, and other uses specific to the nucleic acid sequences.

[0126] Moreover, an “isolated” nucleic acid molecule, such as atranscript/cDNA molecule, can be substantially free of other cellularmaterial, or culture medium when produced by recombinant techniques, orchemical precursors or other chemicals when chemically synthesized.However, the nucleic acid molecule can be fused to other coding orregulatory sequences and still be considered isolated.

[0127] For example, recombinant DNA molecules contained in a vector areconsidered isolated. Further examples of isolated DNA molecules includerecombinant DNA molecules maintained in heterologous host cells orpurified (partially or substantially) DNA molecules in solution.Isolated RNA molecules include in vivo or in vitro RNA transcripts ofthe isolated DNA molecules of the present invention. Isolated nucleicacid molecules according to the present invention further include suchmolecules produced synthetically.

[0128] Accordingly, the present invention provides nucleic acidmolecules that consist of the nucleotide sequence shown in FIG. 1 or 3(SEQ ID NO: 1, transcript sequence and SEQ ID NO:3, genomic sequence),or any nucleic acid molecule that encodes the protein provided in FIG.2, SEQ ID NO:2. A nucleic acid molecule consists of a nucleotidesequence when the nucleotide sequence is the complete nucleotidesequence of the nucleic acid molecule.

[0129] The present invention further provides nucleic acid moleculesthat consist essentially of the nucleotide sequence shown in FIG. 1 or 3(SEQ ID NO:1, transcript sequence and SEQ ID NO:3, genomic sequence), orany nucleic acid molecule that encodes the protein provided in FIG. 2,SEQ ID NO:2. A nucleic acid molecule consists essentially of anucleotide sequence when such a nucleotide sequence is present with onlya few additional nucleic acid residues in the final nucleic acidmolecule.

[0130] The present invention further provides nucleic acid moleculesthat comprise the nucleotide sequences shown in FIG. 1 or 3 (SEQ IDNO:1, transcript sequence and SEQ ID NO:3, genomic sequence), or anynucleic acid molecule that encodes the protein provided in FIG. 2, SEQID NO:2. A nucleic acid molecule comprises a nucleotide sequence whenthe nucleotide sequence is at least part of the final nucleotidesequence of the nucleic acid molecule. In such a fashion, the nucleicacid molecule can be only the nucleotide sequence or have additionalnucleic acid residues, such as nucleic acid residues that are naturallyassociated with it or heterologous nucleotide sequences. Such a nucleicacid molecule can have a few additional nucleotides or can comprisesseveral hundred or more additional nucleotides. A brief description ofhow various types of these nucleic acid molecules can be readilymade/isolated is provided below.

[0131] In FIGS. 1 and 3, both coding and non-coding sequences areprovided. Because of the source of the present invention, humans genomicsequence (FIG. 3) and cDNA/transcript sequences (FIG. 1), the nucleicacid molecules in the Figures will contain genomic intronic sequences,5′ and 3′ non-coding sequences, gene regulatory regions and non-codingintergenic sequences. In general such sequence features are either notedin FIGS. 1 and 3 or can readily be identified using computational toolsknown in the art. As discussed below, some of the non-coding regions,particularly gene regulatory elements such as promoters, are useful fora variety of purposes, e.g. control of heterologous gene expression,target for identifying gene activity modulating compounds, and areparticularly claimed as fragments of the genomic sequence providedherein.

[0132] The isolated nucleic acid molecules can encode the mature proteinplus additional amino or carboxyl-terminal amino acids, or amino acidsinterior to the mature peptide (when the mature form has more than onepeptide chain, for instance). Such sequences may play a role inprocessing of a protein from precursor to a mature form, facilitateprotein trafficking, prolong or shorten protein half-life or facilitatemanipulation of a protein for assay or production, among other things.As generally is the case in situ, the additional amino acids may beprocessed away from the mature protein by cellular enzymes.

[0133] As mentioned above, the isolated nucleic acid molecules include,but are not limited to, the sequence encoding the protease peptidealone, the sequence encoding the mature peptide and additional codingsequences, such as a leader or secretory sequence (e.g., a pre-pro orpro-protein sequence), the sequence encoding the mature peptide, with orwithout the additional coding sequences, plus additional non-codingsequences, for example introns and non-coding 5′ and 3′ sequences suchas transcribed but non-translated sequences that play a role intranscription, mRNA processing (including splicing and polyadenylationsignals), ribosome binding and stability of mRNA. In addition, thenucleic acid molecule may be fused to a marker sequence encoding, forexample, a peptide that facilitates purification.

[0134] Isolated nucleic acid molecules can be in the form of RNA, suchas mRNA, or in the form DNA, including cDNA and genomic DNA obtained bycloning or produced by chemical synthetic techniques or by a combinationthereof. The nucleic acid, especially DNA, can be double-stranded orsingle-stranded. Single-stranded nucleic acid can be the coding strand(sense strand) or the non-coding strand (anti-sense strand).

[0135] The invention further provides nucleic acid molecules that encodefragments of the peptides of the present invention as well as nucleicacid molecules that encode obvious variants of the protease proteins ofthe present invention that are described above. Such nucleic acidmolecules may be naturally occurring, such as allelic variants (samelocus), paralogs (different locus), and orthologs (different organism),or may be constructed by recombinant DNA methods or by chemicalsynthesis. Such non-naturally occurring variants may be made bymutagenesis techniques, including those applied to nucleic acidmolecules, cells, or organisms. Accordingly, as discussed above, thevariants can contain nucleotide substitutions, deletions, inversions andinsertions. Variation can occur in either or both the coding andnon-coding regions. The variations can produce both conservative andnon-conservative amino acid substitutions.

[0136] The present invention further provides non-coding fragments ofthe nucleic acid molecules provided in FIGS. 1 and 3. Preferrednon-coding fragments include, but are not limited to, promotersequences, enhancer sequences, gene modulating sequences and genetermination sequences. Such fragments are useful in controllingheterologous gene expression and in developing screens to identifygene-modulating agents. A promoter can readily be identified as being 5′to the ATG start site in the genomic sequence provided in FIG. 3.

[0137] A fragment comprises a contiguous nucleotide sequence greaterthan 12 or more nucleotides. Further, a fragment could at least 30, 40,50, 100, 250 or 500 nucleotides in length. The length of the fragmentwill be based on its intended use. For example, the fragment can encodeepitope bearing regions of the peptide, or can be useful as DNA probesand primers. Such fragments can be isolated using the known nucleotidesequence to synthesize an oligonucleotide probe. A labeled probe canthen be used to screen a cDNA library, genomic DNA library, or mRNA toisolate nucleic acid corresponding to the coding region. Further,primers can be used in PCR reactions to clone specific regions of gene.

[0138] A probe/primer typically comprises substantially a purifiedoligonucleotide or oligonucleotide pair. The oligonucleotide typicallycomprises a region of nucleotide sequence that hybridizes understringent conditions to at least about 12, 20, 25, 40, 50 or moreconsecutive nucleotides.

[0139] Orthologs, homologs, and allelic variants can be identified usingmethods well known in the art. As described in the Peptide Section,these variants comprise a nucleotide sequence encoding a peptide that istypically 60-70%, 70-80%, 80-90%, and more typically at least about90-95% or more homologous to the nucleotide sequence shown in the Figuresheets or a fragment of this sequence. Such nucleic acid molecules canreadily be identified as being able to hybridize under moderate tostringent conditions, to the nucleotide sequence shown in the Figuresheets or a fragment of the sequence. Allelic variants can readily bedetermined by genetic locus of the encoding gene.

[0140] As used herein, the term “hybridizes under stringent conditions”is intended to describe conditions for hybridization and washing underwhich nucleotide sequences encoding a peptide at least 60-70% homologousto each other typically remain hybridized to each other. The conditionscan be such that sequences at least about 60%, at least about 70%, or atleast about 80% or more homologous to each other typically remainhybridized to each other. Such stringent conditions are known to thoseskilled in the art and can be found in Current Protocols in MolecularBiology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. One example ofstringent hybridization conditions are hybridization in 6×sodiumchloride/sodium citrate (SSC) at about 45C, followed by one or morewashes in 0.2×SSC, 0.1% SDS at 50-65C. Examples of moderate to lowstringency hybridization conditions are well known in the art.

[0141] Nucleic Acid Molecule Uses

[0142] The nucleic acid molecules of the present invention are usefulfor probes, primers, chemical intermediates, and in biological assays.The nucleic acid molecules are useful as a hybridization probe formessenger RNA, transcript/cDNA and genomic DNA to isolate full-lengthcDNA and genomic clones encoding the peptide described in FIG. 2 and toisolate cDNA and genomic clones that correspond to variants (alleles,orthologs, etc.) producing the same or related peptides shown in FIG. 2.Twelve (12) SNPs, including 3 indels, have been identified in the geneencoding the protease protein provided by the present invention and aregiven in FIG. 3.

[0143] The probe can correspond to any sequence along the entire lengthof the nucleic acid molecules provided in the Figures. Accordingly, itcould be derived from 5′ noncoding regions, the coding region, and 3′noncoding regions. However, as discussed, fragments are not to beconstrued as encompassing fragments disclosed prior to the presentinvention.

[0144] The nucleic acid molecules are also useful as primers for PCR toamplify any given region of a nucleic acid molecule and are useful tosynthesize antisense molecules of desired length and sequence.

[0145] The nucleic acid molecules are also useful for constructingrecombinant vectors. Such vectors include expression vectors thatexpress a portion of, or all of, the peptide sequences. Vectors alsoinclude insertion vectors, used to integrate into another nucleic acidmolecule sequence, such as into the cellular genome, to alter in situexpression of a gene and/or gene product. For example, an endogenouscoding sequence can be replaced via homologous recombination with all orpart of the coding region containing one or more specifically introducedmutations.

[0146] The nucleic acid molecules are also useful for expressingantigenic portions of the proteins.

[0147] The nucleic acid molecules are also useful as probes fordetermining the chromosomal positions of the nucleic acid molecules bymeans of in situ hybridization methods. As indicated by the datapresented in FIG. 3, the map position was determined to be on chromosome19 by ePCR, and confirmed with radiation hybrid mapping.

[0148] The nucleic acid molecules are also useful in making vectorscontaining the gene regulatory regions of the nucleic acid molecules ofthe present invention.

[0149] The nucleic acid molecules are also useful for designingribozymes corresponding to all, or a part, of the mRNA produced from thenucleic acid molecules described herein.

[0150] The nucleic acid molecules are also useful for making vectorsthat express part, or all, of the peptides.

[0151] The nucleic acid molecules are also useful for constructing hostcells expressing a part, or all, of the nucleic acid molecules andpeptides.

[0152] The nucleic acid molecules are also useful for constructingtransgenic animals expressing all, or a part, of the nucleic acidmolecules and peptides.

[0153] The nucleic acid molecules are also useful as hybridizationprobes for determining the presence, level, form and distribution ofnucleic acid expression. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. Accordingly, the probes can beused to detect the presence of, or to determine levels of, a specificnucleic acid molecule in cells, tissues, and in organisms. The nucleicacid whose level is determined can be DNA or RNA. Accordingly, probescorresponding to the peptides described herein can be used to assessexpression and/or gene copy number in a given cell, tissue, or organism.These uses are relevant for diagnosis of disorders involving an increaseor decrease in protease protein expression relative to normal results.

[0154] In vitro techniques for detection of mRNA include Northernhybridizations and in situ hybridizations. In vitro techniques fordetecting DNA includes Southern hybridizations and in situhybridization.

[0155] Probes can be used as a part of a diagnostic test kit foridentifying cells or tissues that express a protease protein, such as bymeasuring a level of a protease-encoding nucleic acid in a sample ofcells from a subject e.g., mRNA or genomic DNA, or determining if aprotease gene has been mutated. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor.

[0156] Nucleic acid expression assays are useful for drug screening toidentify compounds that modulate protease nucleic acid expression.

[0157] The invention thus provides a method for identifying a compoundthat can be used to treat a disorder associated with nucleic acidexpression of the protease gene, particularly biological andpathological processes that are mediated by the protease in cells andtissues that express it. Experimental data as provided in FIG. 1indicates that protease proteins of the present invention are expressedin the liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor. Specifically, a virtual northern blot showsexpression in the liver, prostate, T cells from T cell leukemia,hepatocellular carcinoma, and lung tumor. The method typically includesassaying the ability of the compound to modulate the expression of theprotease nucleic acid and thus identifying a compound that can be usedto treat a disorder characterized by undesired protease nucleic acidexpression. The assays can be performed in cell-based and cell-freesystems. Cell-based assays include cells naturally expressing theprotease nucleic acid or recombinant cells genetically engineered toexpress specific nucleic acid sequences.

[0158] The assay for protease nucleic acid expression can involve directassay of nucleic acid levels, such as mRNA levels, or on collateralcompounds involved in the signal pathway. Further, the expression ofgenes that are up- or down-regulated in response to the protease proteinsignal pathway can also be assayed. In this embodiment the regulatoryregions of these genes can be operably linked to a reporter gene such asluciferase.

[0159] Thus, modulators of protease gene expression can be identified ina method wherein a cell is contacted with a candidate compound and theexpression of mRNA determined. The level of expression of protease mRNAin the presence of the candidate compound is compared to the level ofexpression of protease mRNA in the absence of the candidate compound.The candidate compound can then be identified as a modulator of nucleicacid expression based on this comparison and be used, for example totreat a disorder characterized by aberrant nucleic acid expression. Whenexpression of mRNA is statistically significantly greater in thepresence of the candidate compound than in its absence, the candidatecompound is identified as a stimulator of nucleic acid expression. Whennucleic acid expression is statistically significantly less in thepresence of the candidate compound than in its absence, the candidatecompound is identified as an inhibitor of nucleic acid expression.

[0160] The invention further provides methods of treatment, with thenucleic acid as a target, using a compound identified through drugscreening as a gene modulator to modulate protease nucleic acidexpression in cells and tissues that express the protease. Experimentaldata as provided in FIG. 1 indicates that protease proteins of thepresent invention are expressed in the liver, prostate, T cells from Tcell leukemia, hepatocellular carcinoma, and lung tumor. Specifically, avirtual northern blot shows expression in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor.Modulation includes both up-regulation (i.e. activation or agonization)or down-regulation (suppression or antagonization) or nucleic acidexpression.

[0161] Alternatively, a modulator for protease nucleic acid expressioncan be a small molecule or drug identified using the screening assaysdescribed herein as long as the drug or small molecule inhibits theprotease nucleic acid expression in the cells and tissues that expressthe protein. Experimental data as provided in FIG. 1 indicates thatprotease proteins of the present invention are expressed in the liver,prostate, T cells from T cell leukemia, hepatocellular carcinoma, andlung tumor. Specifically, a virtual northern blot shows expression inthe liver, prostate, T cells from T cell leukemia, hepatocellularcarcinoma, and lung tumor.

[0162] The nucleic acid molecules are also useful for monitoring theeffectiveness of modulating compounds on the expression or activity ofthe protease gene in clinical trials or in a treatment regimen. Thus,the gene expression pattern can serve as a barometer for the continuingeffectiveness of treatment with the compound, particularly withcompounds to which a patient can develop resistance. The gene expressionpattern can also serve as a marker indicative of a physiologicalresponse of the affected cells to the compound. Accordingly, suchmonitoring would allow either increased administration of the compoundor the administration of alternative compounds to which the patient hasnot become resistant. Similarly, if the level of nucleic acid expressionfalls below a desirable level, administration of the compound could becommensurately decreased.

[0163] The nucleic acid molecules are also useful in diagnostic assaysfor qualitative changes in protease nucleic acid expression, andparticularly in qualitative changes that lead to pathology. The nucleicacid molecules can be used to detect mutations in protease genes andgene expression products such as mRNA. The nucleic acid molecules can beused as hybridization probes to detect naturally occurring geneticmutations in the protease gene and thereby to determine whether asubject with the mutation is at risk for a disorder caused by themutation. Mutations include deletion, addition, or substitution of oneor more nucleotides in the gene, chromosomal rearrangement, such asinversion or transposition, modification of genomic DNA, such asaberrant methylation patterns or changes in gene copy number, such asamplification. Detection of a mutated form of the protease geneassociated with a dysfunction provides a diagnostic tool for an activedisease or susceptibility to disease when the disease results fromoverexpression, underexpression, or altered expression of a proteaseprotein.

[0164] Individuals carrying mutations in the protease gene can bedetected at the nucleic acid level by a variety of techniques. FIG. 3provides information on SNPs that have been identified in a geneencoding the protease protein of the present invention. Twelve (12) SNPvariants were found, including 3 indels (indicated by a “-”) and 1 SNPin exons, none of which cause changes in the amino acid sequence. Asindicated by the data presented in FIG. 3, the map position wasdetermined to be on chromosome 19 by ePCR, and confirmed with radiationhybrid mapping. Genomic DNA can be analyzed directly or can be amplifiedby using PCR prior to analysis. RNA or cDNA can be used in the same way.In some uses, detection of the mutation involves the use of aprobe/primer in a polymerase chain reaction (PCR) (see, e.g. U.S. Pat.Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or,alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegranet al., Science 241:1077-1080 (1988); and Nakazawa et al., PNAS91:360-364 (1994)), the latter of which can be particularly useful fordetecting point mutations in the gene (see Abravaya et al., NucleicAcids Res. 23:675-682 (1995)). This method can include the steps ofcollecting a sample of cells from a patient, isolating nucleic acid(e.g., genomic, mRNA or both) from the cells of the sample, contactingthe nucleic acid sample with one or more primers which specificallyhybridize to a gene under conditions such that hybridization andamplification of the gene (if present) occurs, and detecting thepresence or absence of an amplification product, or detecting the sizeof the amplification product and comparing the length to a controlsample. Deletions and insertions can be detected by a change in size ofthe amplified product compared to the normal genotype. Point mutationscan be identified by hybridizing amplified DNA to normal RNA orantisense DNA sequences.

[0165] Alternatively, mutations in a protease gene can be directlyidentified, for example, by alterations in restriction enzyme digestionpatterns determined by gel electrophoresis.

[0166] Further, sequence-specific ribozymes (U.S. Pat. No. 5,498,531)can be used to score for the presence of specific mutations bydevelopment or loss of a ribozyme cleavage site. Perfectly matchedsequences can be distinguished from mismatched sequences by nucleasecleavage digestion assays or by differences in melting temperature.

[0167] Sequence changes at specific locations can also be assessed bynuclease protection assays such as RNase and S1 protection or thechemical cleavage method. Furthermore, sequence differences between amutant protease gene and a wild-type gene can be determined by directDNA sequencing. A variety of automated sequencing procedures can beutilized when performing the diagnostic assays (Naeve, C. W., (1995)Biotechniques 19:448), including sequencing by mass spectrometry (see,e.g., PCT International Publication No. WO 94/16101; Cohen et al., Adv.Chromatogr. 36:127-162 (1996); and Griffin et al., Appl. Biochem.Biotechnol. 38:147-159 (1993)).

[0168] Other methods for detecting mutations in the gene include methodsin which protection from cleavage agents is used to detect mismatchedbases in RNA/RNA or RNA/DNA duplexes (Myers et al., Science 230:1242(1985)); Cotton et al., PNAS 85:4397 (1988); Saleeba et al., Meth.Enzymol. 217:286-295 (1992)), electrophoretic mobility of mutant andwild type nucleic acid is compared (Orita et al., PNAS 86:2766 (1989);Cotton et al., Mutat. Res. 285:125-144 (1993); and Hayashi et al.,Genet. Anal. Tech. Appl. 9:73-79 (1992)), and movement of mutant orwild-type fragments in polyacrylamide gels containing a gradient ofdenaturant is assayed using denaturing gradient gel electrophoresis(Myers et al., Nature 313:495 (1985)). Examples of other techniques fordetecting point mutations include selective oligonucleotidehybridization, selective amplification, and selective primer extension.

[0169] The nucleic acid molecules are also useful for testing anindividual for a genotype that while not necessarily causing thedisease, nevertheless affects the treatment modality. Thus, the nucleicacid molecules can be used to study the relationship between anindividual's genotype and the individual's response to a compound usedfor treatment (pharmacogenomic relationship). Accordingly, the nucleicacid molecules described herein can be used to assess the mutationcontent of the protease gene in an individual in order to select anappropriate compound or dosage regimen for treatment.

[0170] Thus nucleic acid molecules displaying genetic variations thataffect treatment provide a diagnostic target that can be used to tailortreatment in an individual. Accordingly, the production of recombinantcells and animals containing these polymorphisms allow effectiveclinical design of treatment compounds and dosage regimens.

[0171] The nucleic acid molecules are thus useful as antisenseconstructs to control protease gene expression in cells, tissues, andorganisms. A DNA antisense nucleic acid molecule is designed to becomplementary to a region of the gene involved in transcription,preventing transcription and hence production of protease protein. Anantisense RNA or DNA nucleic acid molecule would hybridize to the mRNAand thus block translation of mRNA into protease protein. FIG. 3provides information on SNPs that have been identified in a geneencoding the protease protein of the present invention. Twelve (12) SNPvariants were found, including 3 indels (indicated by a “-”) and 1 SNPin exons, none of which cause changes in the amino acid sequence.

[0172] Alternatively, a class of antisense molecules can be used toinactivate mRNA in order to decrease expression of protease nucleicacid. Accordingly, these molecules can treat a disorder characterized byabnormal or undesired protease nucleic acid expression. This techniqueinvolves cleavage by means of ribozymes containing nucleotide sequencescomplementary to one or more regions in the mRNA that attenuate theability of the mRNA to be translated. Possible regions include codingregions and particularly coding regions corresponding to the catalyticand other functional activities of the protease protein, such assubstrate binding.

[0173] The nucleic acid molecules also provide vectors for gene therapyin patients containing cells that are aberrant in protease geneexpression. Thus, recombinant cells, which include the patient's cellsthat have been engineered ex vivo and returned to the patient, areintroduced into an individual where the cells produce the desiredprotease protein to treat the individual.

[0174] The invention also encompasses kits for detecting the presence ofa protease nucleic acid in a biological sample. Experimental data asprovided in FIG. 1 indicates that protease proteins of the presentinvention are expressed in the liver, prostate, T cells from T cellleukemia, hepatocellular carcinoma, and lung tumor. Specifically, avirtual northern blot shows expression in the liver, prostate, T cellsfrom T cell leukemia, hepatocellular carcinoma, and lung tumor. Forexample, the kit can comprise reagents such as a labeled or labelablenucleic acid or agent capable of detecting protease nucleic acid in abiological sample; means for determining the amount of protease nucleicacid in the sample; and means for comparing the amount of proteasenucleic acid in the sample with a standard. The compound or agent can bepackaged in a suitable container. The kit can further compriseinstructions for using the kit to detect protease protein mRNA or DNA.

[0175] Nucleic Acid Arrays

[0176] The present invention further provides nucleic acid detectionkits, such as arrays or microarrays of nucleic acid molecules that arebased on the sequence information provided in FIGS. 1 and 3 (SEQ IDNOS:1 and 3).

[0177] As used herein “Arrays” or “Microarrays” refers to an array ofdistinct polynucleotides or oligonucleotides synthesized on a substrate,such as paper, nylon or other type of membrane, filter, chip, glassslide, or any other suitable solid support. In one embodiment, themicroarray is prepared and used according to the methods described inU.S. Pat. No. 5,837,832, Chee et al., PCT application WO95/11995 (Cheeet al.), Lockhart, D. J. et al. (1996; Nat. Biotech. 14: 1675-1680) andSchena, M. et al. (1996; Proc. Natl. Acad. Sci. 93: 10614-10619), all ofwhich are incorporated herein in their entirety by reference. In otherembodiments, such arrays are produced by the methods described by Brownet al., U.S. Pat. No. 5,807,522.

[0178] The microarray or detection kit is preferably composed of a largenumber of unique, single-stranded nucleic acid sequences, usually eithersynthetic antisense oligonucleotides or fragments of cDNAs, fixed to asolid support. The oligonucleotides are preferably about 6-60nucleotides in length, more preferably 15-30 nucleotides in length, andmost preferably about 20-25 nucleotides in length. For a certain type ofmicroarray or detection kit, it may be preferable to useoligonucleotides that are only 7-20 nucleotides in length. Themicroarray or detection kit may contain oligonucleotides that cover theknown 5′, or 3′, sequence, sequential oligonucleotides which cover thefull length sequence; or unique oligonucleotides selected fromparticular areas along the length of the sequence. Polynucleotides usedin the microarray or detection kit may be oligonucleotides that arespecific to a gene or genes of interest.

[0179] In order to produce oligonucleotides to a known sequence for amicroarray or detection kit, the gene(s) of interest (or an ORFidentified from the contigs of the present invention) is typicallyexamined using a computer algorithm which starts at the 5′ or at the 3′end of the nucleotide sequence. Typical algorithms will then identifyoligomers of defined length that are unique to the gene, have a GCcontent within a range suitable for hybridization, and lack predictedsecondary structure that may interfere with hybridization. In certainsituations it may be appropriate to use pairs of oligonucleotides on amicroarray or detection kit. The “pairs” will be identical, except forone nucleotide that preferably is located in the center of the sequence.The second oligonucleotide in the pair (mismatched by one) serves as acontrol. The number of oligonucleotide pairs may range from two to onemillion. The oligomers are synthesized at designated areas on asubstrate using a light-directed chemical process. The substrate may bepaper, nylon or other type of membrane, filter, chip, glass slide or anyother suitable solid support.

[0180] In another aspect, an oligonucleotide may be synthesized on thesurface of the substrate by using a chemical coupling procedure and anink jet application apparatus, as described in PCT applicationWO95/251116 (Baldeschweiler et al.) which is incorporated herein in itsentirety by reference. In another aspect, a “gridded” array analogous toa dot (or slot) blot may be used to arrange and link cDNA fragments oroligonucleotides to the surface of a substrate using a vacuum system,thermal, UV, mechanical or chemical bonding procedures. An array, suchas those described above, may be produced by hand or by using availabledevices (slot blot or dot blot apparatus), materials (any suitable solidsupport), and machines (including robotic instruments), and may contain8, 24, 96, 384, 1536, 6144 or more oligonucleotides, or any other numberbetween two and one million which lends itself to the efficient use ofcommercially available instrumentation.

[0181] In order to conduct sample analysis using a microarray ordetection kit, the RNA or DNA from a biological sample is made intohybridization probes. The mRNA is isolated, and cDNA is produced andused as a template to make antisense RNA (aRNA). The aRNA is amplifiedin the presence of fluorescent nucleotides, and labeled probes areincubated with the microarray or detection kit so that the probesequences hybridize to complementary oligonucleotides of the microarrayor detection kit. Incubation conditions are adjusted so thathybridization occurs with precise complementary matches or with variousdegrees of less complementarity. After removal of nonhybridized probes,a scanner is used to determine the levels and patterns of fluorescence.The scanned images are examined to determine degree of complementarityand the relative abundance of each oligonucleotide sequence on themicroarray or detection kit. The biological samples may be obtained fromany bodily fluids (such as blood, urine, saliva, phlegm, gastric juices,etc.), cultured cells, biopsies, or other tissue preparations. Adetection system may be used to measure the absence, presence, andamount of hybridization for all of the distinct sequencessimultaneously. This data may be used for large-scale correlationstudies on the sequences, expression patterns, mutations, variants, orpolymorphisms among samples.

[0182] Using such arrays, the present invention provides methods toidentify the expression of the protease proteins/peptides of the presentinvention. In detail, such methods comprise incubating a test samplewith one or more nucleic acid molecules and assaying for binding of thenucleic acid molecule with components within the test sample. Suchassays will typically involve arrays comprising many genes, at least oneof which is a gene of the present invention and or alleles of theprotease gene of the present invention. FIG. 3 provides information onSNPs that have been identified in a gene encoding the protease proteinof the present invention. Twelve (12) SNP variants were found, including3 indels (indicated by a “-”) and 1 SNP in exons, none of which causechanges in the amino acid sequence.

[0183] Conditions for incubating a nucleic acid molecule with a testsample vary. Incubation conditions depend on the format employed in theassay, the detection methods employed, and the type and nature of thenucleic acid molecule used in the assay. One skilled in the art willrecognize that any one of the commonly available hybridization,amplification or array assay formats can readily be adapted to employthe novel fragments of the Human genome disclosed herein. Examples ofsuch assays can be found in Chard, T, An Introduction toRadioimmunoassay and Related Techniques, Elsevier Science Publishers,Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques inImmunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2(1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of EnzymeImmunoassays: Laboratory Techniques in Biochemistry and MolecularBiology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985).

[0184] The test samples of the present invention include cells, proteinor membrane extracts of cells. The test sample used in theabove-described method will vary based on the assay format, nature ofthe detection method and the tissues, cells or extracts used as thesample to be assayed. Methods for preparing nucleic acid extracts or ofcells are well known in the art and can be readily be adapted in orderto obtain a sample that is compatible with the system utilized.

[0185] In another embodiment of the present invention, kits are providedwhich contain the necessary reagents to carry out the assays of thepresent invention.

[0186] Specifically, the invention provides a compartmentalized kit toreceive, in close confinement, one or more containers which comprises:(a) a first container comprising one of the nucleic acid molecules thatcan bind to a fragment of the Human genome disclosed herein; and (b) oneor more other containers comprising one or more of the following: washreagents, reagents capable of detecting presence of a bound nucleicacid.

[0187] In detail, a compartmentalized kit includes any kit in whichreagents are contained in separate containers. Such containers includesmall glass containers, plastic containers, strips of plastic, glass orpaper, or arraying material such as silica. Such containers allows oneto efficiently transfer reagents from one compartment to anothercompartment such that the samples and reagents are notcross-contaminated, and the agents or solutions of each container can beadded in a quantitative fashion from one compartment to another. Suchcontainers will include a container which will accept the test sample, acontainer which contains the nucleic acid probe, containers whichcontain wash reagents (such as phosphate buffered saline, Tris-buffers,etc.), and containers which contain the reagents used to detect thebound probe. One skilled in the art will readily recognize that thepreviously unidentified protease gene of the present invention can beroutinely identified using the sequence information disclosed herein canbe readily incorporated into one of the established kit formats whichare well known in the art, particularly expression arrays.

[0188] Vectors/Host Cells

[0189] The invention also provides vectors containing the nucleic acidmolecules described herein. The term “vector” refers to a vehicle,preferably a nucleic acid molecule, which can transport the nucleic acidmolecules. When the vector is a nucleic acid molecule, the nucleic acidmolecules are covalently linked to the vector nucleic acid. With thisaspect of the invention, the vector includes a plasmid, single or doublestranded phage, a single or double stranded RNA or DNA viral vector, orartificial chromosome, such as a BAC, PAC, YAC, OR MAC.

[0190] A vector can be maintained in the host cell as anextrachromosomal element where it replicates and produces additionalcopies of the nucleic acid molecules. Alternatively, the vector mayintegrate into the host cell genome and produce additional copies of thenucleic acid molecules when the host cell replicates.

[0191] The invention provides vectors for the maintenance (cloningvectors) or vectors for expression (expression vectors) of the nucleicacid molecules. The vectors can function in prokaryotic or eukaryoticcells or in both (shuttle vectors).

[0192] Expression vectors contain cis-acting regulatory regions that areoperably linked in the vector to the nucleic acid molecules such thattranscription of the nucleic acid molecules is allowed in a host cell.The nucleic acid molecules can be introduced into the host cell with aseparate nucleic acid molecule capable of affecting transcription. Thus,the second nucleic acid molecule may provide a trans-acting factorinteracting with the cis-regulatory control region to allowtranscription of the nucleic acid molecules from the vector.Alternatively, a trans-acting factor may be supplied by the host cell.Finally, a trans-acting factor can be produced from the vector itself.It is understood, however, that in some embodiments, transcriptionand/or translation of the nucleic acid molecules can occur in acell-free system.

[0193] The regulatory sequence to which the nucleic acid moleculesdescribed herein can be operably linked include promoters for directingmRNA transcription. These include, but are not limited to, the leftpromoter from bacteriophage λ, the lac, TRP, and TAC promoters from E.coli, the early and late promoters from SV40, the CMV immediate earlypromoter, the adenovirus early and late promoters, and retroviruslong-terminal repeats.

[0194] In addition to control regions that promote transcription,expression vectors may also include regions that modulate transcription,such as repressor binding sites and enhancers. Examples include the SV40enhancer, the cytomegalovirus immediate early enhancer, polyomaenhancer, adenovirus enhancers, and retrovirus LTR enhancers.

[0195] In addition to containing sites for transcription initiation andcontrol, expression vectors can also contain sequences necessary fortranscription termination and, in the transcribed region a ribosomebinding site for translation. Other regulatory control elements forexpression include initiation and termination codons as well aspolyadenylation signals. The person of ordinary skill in the art wouldbe aware of the numerous regulatory sequences that are useful inexpression vectors. Such regulatory sequences are described, forexample, in Sambrook et al., Molecular Cloning: A Laboratory Manual.2nd. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,(1989).

[0196] A variety of expression vectors can be used to express a nucleicacid molecule. Such vectors include chromosomal, episomal, andvirus-derived vectors, for example vectors derived from bacterialplasmids, from bacteriophage, from yeast episomes, from yeastchromosomal elements, including yeast artificial chromosomes, fromviruses such as baculoviruses, papovaviruses such as SV40, Vacciniaviruses, adenoviruses, poxviruses, pseudorabies viruses, andretroviruses. Vectors may also be derived from combinations of thesesources such as those derived from plasmid and bacteriophage geneticelements, e.g. cosmids and phagemids. Appropriate cloning and expressionvectors for prokaryotic and eukaryotic hosts are described in Sambrooket al., Molecular Cloning: A Laboratory Manual. 2nd. ed., Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., (1989).

[0197] The regulatory sequence may provide constitutive expression inone or more host cells (i.e. tissue specific) or may provide forinducible expression in one or more cell types such as by temperature,nutrient additive, or exogenous factor such as a hormone or otherligand. A variety of vectors providing for constitutive and inducibleexpression in prokaryotic and eukaryotic hosts are well known to thoseof ordinary skill in the art.

[0198] The nucleic acid molecules can be inserted into the vectornucleic acid by well-known methodology. Generally, the DNA sequence thatwill ultimately be expressed is joined to an expression vector bycleaving the DNA sequence and the expression vector with one or morerestriction enzymes and then ligating the fragments together. Proceduresfor restriction enzyme digestion and ligation are well known to those ofordinary skill in the art.

[0199] The vector containing the appropriate nucleic acid molecule canbe introduced into an appropriate host cell for propagation orexpression using well-known techniques. Bacterial cells include, but arenot limited to, E. coli, Streptomyces, and Salmonella typhimurium.Eukaryotic cells include, but are not limited to, yeast, insect cellssuch as Drosophila, animal cells such as COS and CHO cells, and plantcells.

[0200] As described herein, it may be desirable to express the peptideas a fusion protein. Accordingly, the invention provides fusion vectorsthat allow for the production of the peptides. Fusion vectors canincrease the expression of a recombinant protein, increase thesolubility of the recombinant protein, and aid in the purification ofthe protein by acting for example as a ligand for affinity purification.A proteolytic cleavage site may be introduced at the junction of thefusion moiety so that the desired peptide can ultimately be separatedfrom the fusion moiety. Proteolytic enzymes include, but are not limitedto, factor Xa, thrombin, and enteroprotease. Typical fusion expressionvectors include pGEX (Smith et al., Gene 67:31-40 (1988)), pMAL (NewEngland Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.)which fuse glutathione S-transferase (GST), maltose E binding protein,or protein A, respectively, to the target recombinant protein. Examplesof suitable inducible non-fusion E. coli expression vectors include pTrc(Amann et al., Gene 69:301-315 (1988)) and pET 11d (Studier et al., GeneExpression Technology: Methods in Enzymology 185:60-89 (1990)).

[0201] Recombinant protein expression can be maximized in host bacteriaby providing a genetic background wherein the host cell has an impairedcapacity to proteolytically cleave the recombinant protein. (Gottesman,S., Gene Expression Technology: Methods in Enzymology 185, AcademicPress, San Diego, Calif. (1990)119-128). Alternatively, the sequence ofthe nucleic acid molecule of interest can be altered to providepreferential codon usage for a specific host cell, for example E. coli.(Wada et al., Nucleic Acids Res. 20:2111-2118 (1992)).

[0202] The nucleic acid molecules can also be expressed by expressionvectors that are operative in yeast. Examples of vectors for expressionin yeast e.g., S. cerevisiae include pYepSec1 (Baldari, et al., EMBO J.6:229-234 (1987)), pMFa (Kujan et al., Cell 30:933 943(1982)), pJRY88(Schultz et al., Gene 54:113-123 (1987)), and pYES2 (InvitrogenCorporation, San Diego, Calif.).

[0203] The nucleic acid molecules can also be expressed in insect cellsusing, for example, baculovirus expression vectors. Baculovirus vectorsavailable for expression of proteins in cultured insect cells (e.g., Sf9cells) include the pAc series (Smith et al., Mol. Cell Biol. 3:2156-2165(1983)) and the pVL series (Lucklow et al., Virology 170:31-39 (1989)).

[0204] In certain embodiments of the invention, the nucleic acidmolecules described herein are expressed in mammalian cells usingmammalian expression vectors. Examples of mammalian expression vectorsinclude pCDM8 (Seed, B. Nature 329:840(1987)) and pMT2PC (Kaufman etal., EMBO J. 6:187-195 (1987)).

[0205] The expression vectors listed herein are provided by way ofexample only of the well-known vectors available to those of ordinaryskill in the art that would be useful to express the nucleic acidmolecules. The person of ordinary skill in the art would be aware ofother vectors suitable for maintenance propagation or expression of thenucleic acid molecules described herein. These are found for example inSambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: ALaboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

[0206] The invention also encompasses vectors in which the nucleic acidsequences described herein are cloned into the vector in reverseorientation, but operably linked to a regulatory sequence that permitstranscription of antisense RNA. Thus, an antisense transcript can beproduced to all, or to a portion, of the nucleic acid molecule sequencesdescribed herein, including both coding and non-coding regions.Expression of this antisense RNA is subject to each of the parametersdescribed above in relation to expression of the sense RNA (regulatorysequences, constitutive or inducible expression, tissue-specificexpression).

[0207] The invention also relates to recombinant host cells containingthe vectors described herein. Host cells therefore include prokaryoticcells, lower eukaryotic cells such as yeast, other eukaryotic cells suchas insect cells, and higher eukaryotic cells such as mammalian cells.

[0208] The recombinant host cells are prepared by introducing the vectorconstructs described herein into the cells by techniques readilyavailable to the person of ordinary skill in the art. These include, butare not limited to, calcium phosphate transfection,DEAE-dextran-mediated transfection, cationic lipid-mediatedtransfection, electroporation, transduction, infection, lipofection, andother techniques such as those found in Sambrook, et al. (MolecularCloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).

[0209] Host cells can contain more than one vector. Thus, differentnucleotide sequences can be introduced on different vectors of the samecell. Similarly, the nucleic acid molecules can be introduced eitheralone or with other nucleic acid molecules that are not related to thenucleic acid molecules such as those providing trans-acting factors forexpression vectors. When more than one vector is introduced into a cell,the vectors can be introduced independently, co-introduced or joined tothe nucleic acid molecule vector.

[0210] In the case of bacteriophage and viral vectors, these can beintroduced into cells as packaged or encapsulated virus by standardprocedures for infection and transduction. Viral vectors can bereplication-competent or replication-defective. In the case in whichviral replication is defective, replication will occur in host cellsproviding functions that complement the defects.

[0211] Vectors generally include selectable markers that enable theselection of the subpopulation of cells that contain the recombinantvector constructs. The marker can be contained in the same vector thatcontains the nucleic acid molecules described herein or may be on aseparate vector. Markers include tetracycline or ampicillin-resistancegenes for prokaryotic host cells and dihydrofolate reductase or neomycinresistance for eukaryotic host cells. However, any marker that providesselection for a phenotypic trait will be effective.

[0212] While the mature proteins can be produced in bacteria, yeast,mammalian cells, and other cells under the control of the appropriateregulatory sequences, cell-free transcription and translation systemscan also be used to produce these proteins using RNA derived from theDNA constructs described herein.

[0213] Where secretion of the peptide is desired, which is difficult toachieve with multi-transmembrane domain containing proteins such asproteases, appropriate secretion signals are incorporated into thevector. The signal sequence can be endogenous to the peptides orheterologous to these peptides.

[0214] Where the peptide is not secreted into the medium, which istypically the case with proteases, the protein can be isolated from thehost cell by standard disruption procedures, including freeze thaw,sonication, mechanical disruption, use of lysing agents and the like.The peptide can then be recovered and purified by well-knownpurification methods including ammonium sulfate precipitation, acidextraction, anion or cationic exchange chromatography, phosphocellulosechromatography, hydrophobic-interaction chromatography, affinitychromatography, hydroxylapatite chromatography, lectin chromatography,or high performance liquid chromatography.

[0215] It is also understood that depending upon the host cell inrecombinant production of the peptides described herein, the peptidescan have various glycosylation patterns, depending upon the cell, ormaybe non-glycosylated as when produced in bacteria. In addition, thepeptides may include an initial modified methionine in some cases as aresult of a host-mediated process.

[0216] Uses of Vectors and Host Cells

[0217] The recombinant host cells expressing the peptides describedherein have a variety of uses. First, the cells are useful for producinga protease protein or peptide that can be further purified to producedesired amounts of protease protein or fragments. Thus, host cellscontaining expression vectors are useful for peptide production. Hostcells are also useful for conducting cell-based assays involving theprotease protein or protease protein fragments, such as those describedabove as well as other formats known in the art. Thus, a recombinanthost cell expressing a native protease protein is useful for assayingcompounds that stimulate or inhibit protease protein function.

[0218] Host cells are also useful for identifying protease proteinmutants in which these functions are affected. If the mutants naturallyoccur and give rise to a pathology, host cells containing the mutationsare useful to assay compounds that have a desired effect on the mutantprotease protein (for example, stimulating or inhibiting function) whichmay not be indicated by their effect on the native protease protein.

[0219] Genetically engineered host cells can be further used to producenon-human transgenic animals. A transgenic animal is preferably amammal, for example a rodent, such as a rat or mouse, in which one ormore of the cells of the animal include a transgene. A transgene isexogenous DNA which is integrated into the genome of a cell from which atransgenic animal develops and which remains in the genome of the matureanimal in one or more cell types or tissues of the transgenic animal.These animals are useful for studying the function of a protease proteinand identifying and evaluating modulators of protease protein activity.Other examples of transgenic animals include non-human primates, sheep,dogs, cows, goats, chickens, and amphibians.

[0220] A transgenic animal can be produced by introducing nucleic acidinto the male pronuclei of a fertilized oocyte, e.g., by microinjection,retroviral infection, and allowing the oocyte to develop in apseudopregnant female foster animal. Any of the protease proteinnucleotide sequences can be introduced as a transgene into the genome ofa non-human animal, such as a mouse.

[0221] Any of the regulatory or other sequences useful in expressionvectors can form part of the transgenic sequence. This includes intronicsequences and polyadenylation signals, if not already included. Atissue-specific regulatory sequence(s) can be operably linked to thetransgene to direct expression of the protease protein to particularcells.

[0222] Methods for generating transgenic animals via embryo manipulationand microinjection, particularly animals such as mice, have becomeconventional in the art and are described, for example, in U.S. Pat.Nos. 4,736,866 and 4,870,009, both by Leder et al., U.S. Pat. No.4,873,191 by Wagner et al. and in Hogan, B., Manipulating the MouseEmbryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1986). Similar methods are used for production of other transgenicanimals. A transgenic founder animal can be identified based upon thepresence of the transgene in its genome and/or expression of transgenicmRNA in tissues or cells of the animals. A transgenic founder animal canthen be used to breed additional animals carrying the transgene.Moreover, transgenic animals carrying a transgene can further be bred toother transgenic animals carrying other transgenes. A transgenic animalalso includes animals in which the entire animal or tissues in theanimal have been produced using the homologously recombinant host cellsdescribed herein.

[0223] In another embodiment, transgenic non-human animals can beproduced which contain selected systems that allow for regulatedexpression of the transgene. One example of such a system is thecre/loxP recombinase system of bacteriophage P1. For a description ofthe cre/loxP recombinase system, see, e.g., Lakso et al. PNAS89:6232-6236 (1992). Another example of a recombinase system is the FLPrecombinase system of S. cerevisiae (O'Gorman et al. Science251:1351-1355 (1991). If a cre/loxP recombinase system is used toregulate expression of the transgene, animals containing transgenesencoding both the Cre recombinase and a selected protein is required.Such animals can be provided through the construction of “double”transgenic animals, e.g., by mating two transgenic animals, onecontaining a transgene encoding a selected protein and the othercontaining a transgene encoding a recombinase.

[0224] Clones of the non-human transgenic animals described herein canalso be produced according to the methods described in Wilmut, I. et al.Nature 385:810-813 (1997) and PCT International Publication Nos. WO97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic cell, fromthe transgenic animal can be isolated and induced to exit the growthcycle and enter G_(o) phase. The quiescent cell can then be fused, e.g.,through the use of electrical pulses, to an enucleated oocyte from ananimal of the same species from which the quiescent cell is isolated.The reconstructed oocyte is then cultured such that it develops tomorula or blastocyst and then transferred to pseudopregnant femalefoster animal. The offspring born of this female foster animal will be aclone of the animal from which the cell, e.g., the somatic cell, isisolated.

[0225] Transgenic animals containing recombinant cells that express thepeptides described herein are useful to conduct the assays describedherein in an in vivo context. Accordingly, the various physiologicalfactors that are present in vivo and that could effect substratebinding, protease protein activity/activation, and signal transduction,may not be evident from in vitro cell-free or cell-based assays.Accordingly, it is useful to provide non-human transgenic animals toassay in vivo protease protein function, including substrateinteraction, the effect of specific mutant protease proteins on proteaseprotein function and substrate interaction, and the effect of chimericprotease proteins. It is also possible to assess the effect of nullmutations, that is mutations that substantially or completely eliminateone or more protease protein functions.

[0226] All publications and patents mentioned in the above specificationare herein incorporated by reference. Various modifications andvariations of the described method and system of the invention will beapparent to those skilled in the art without departing from the scopeand spirit of the invention. Although the invention has been describedin connection with specific preferred embodiments, it should beunderstood that the invention as claimed should not be unduly limited tosuch specific embodiments. Indeed, various modifications of theabove-described modes for carrying out the invention which are obviousto those skilled in the field of molecular biology or related fields areintended to be within the scope of the following claims.

1 16 1 1615 DNA HUMAN 1 tgggcacctg gttgttcaca cggcagggga ggaacagccctgtcaactgc tggccccggg 60 aaactgggcc tggggaggac atgcttgggc ataataagttagccctgggg gcagggcaga 120 gctggcctcg ggcccagacc ctgccgcaat gaggacaggcctggctgtgg ccccagcatg 180 gtgtctgttg caggtggccg gactgtgcca tgctgctccagacccaaggt ggcagctctc 240 actgcgggga ccctgctact tctgacagcc atcggggcggcatcctgggc cattgtggct 300 gttctcctca ggagtgacca ggagccgctg tacccagtgcaggtcagctc tgcggacgct 360 cggctcatgg tctttgacaa gacggaaggg acgtggcggctgctgtgctc ctcgcgctcc 420 aacgccaggg tagccggact cagctgcgag gagatgggcttcctcagtga ttgccccaga 480 ggccgtttct tggccgccat ctgccaagac tgtggccgcaggaagctgcc cgtggaccgc 540 atcgtgggag gccgggacac cagcttgggc cggtggccgtggcaagtcag ccttcgctat 600 gatggagcac acctctgtgg gggatccctg ctctccggggactgggtgct gacagccgcc 660 cactgcttcc cggagcggaa ccgggtcctg tcccgatggcgagtgtttgc cggtgccgtg 720 gcccaggcct ctccccacgg tctgcagctg ggggtgcaggctgtggtcta ccacgggggc 780 tatcttccct ttcgggaccc caacagcgag gagaacagcaacgatattgc cctggtccac 840 ctctccagtc ccctgcccct cacagaatac atccagcctgtgtgcctccc agctgccggc 900 caggccctgg tggatggcaa gatctgtacc gtgacgggctggggcaacac gcagtactat 960 ggccaacagg ccggggtact ccaggaggct cgagtccccataatcagcaa tgatgtctgc 1020 aatggcgctg acttctatgg aaaccagatc aagcccaagatgttctgtgc tggctacccc 1080 gagggtggca ttgatgcctg ccagggcgac agcggtggtccctttgtgtg tgaggacagc 1140 atctctcgga cgccacgttg gcggctgtgt ggcattgtgagttggggcac tggctgtgcc 1200 ctggcccaga agccaggcgt ctacaccaaa gtcagtgacttccgggagtg gatcttccag 1260 gccataaaga ctcactccga agccagcggc atggtgacccagctctgacc ggtggcttct 1320 cgctgcgcag cctccagggc ccgaggtgat cccggtggtgggatccacgc tgggccgagg 1380 atgggacgtt tttcttcttg ggcccggtcc acaggtccaaggacaccctc cctccagggt 1440 cctctcttcc acagtggcgg gcccactcag ccccgagaccacccaacctc accctcctga 1500 cccccatgta aatattgttc tgctgtctgg gactcctgtctaggtgcccc tgatgatggg 1560 atgctcttta aataataaag atggttttga ttaaaaaaaaaaaaaaaaaa aaaaa 1615 2 376 PRT HUMAN 2 Met Val Ser Val Ala Gly Gly ArgThr Val Pro Cys Cys Ser Arg Pro 1 5 10 15 Lys Val Ala Ala Leu Thr AlaGly Thr Leu Leu Leu Leu Thr Ala Ile 20 25 30 Gly Ala Ala Ser Trp Ala IleVal Ala Val Leu Leu Arg Ser Asp Gln 35 40 45 Glu Pro Leu Tyr Pro Val GlnVal Ser Ser Ala Asp Ala Arg Leu Met 50 55 60 Val Phe Asp Lys Thr Glu GlyThr Trp Arg Leu Leu Cys Ser Ser Arg 65 70 75 80 Ser Asn Ala Arg Val AlaGly Leu Ser Cys Glu Glu Met Gly Phe Leu 85 90 95 Ser Asp Cys Pro Arg GlyArg Phe Leu Ala Ala Ile Cys Gln Asp Cys 100 105 110 Gly Arg Arg Lys LeuPro Val Asp Arg Ile Val Gly Gly Arg Asp Thr 115 120 125 Ser Leu Gly ArgTrp Pro Trp Gln Val Ser Leu Arg Tyr Asp Gly Ala 130 135 140 His Leu CysGly Gly Ser Leu Leu Ser Gly Asp Trp Val Leu Thr Ala 145 150 155 160 AlaHis Cys Phe Pro Glu Arg Asn Arg Val Leu Ser Arg Trp Arg Val 165 170 175Phe Ala Gly Ala Val Ala Gln Ala Ser Pro His Gly Leu Gln Leu Gly 180 185190 Val Gln Ala Val Val Tyr His Gly Gly Tyr Leu Pro Phe Arg Asp Pro 195200 205 Asn Ser Glu Glu Asn Ser Asn Asp Ile Ala Leu Val His Leu Ser Ser210 215 220 Pro Leu Pro Leu Thr Glu Tyr Ile Gln Pro Val Cys Leu Pro AlaAla 225 230 235 240 Gly Gln Ala Leu Val Asp Gly Lys Ile Cys Thr Val ThrGly Trp Gly 245 250 255 Asn Thr Gln Tyr Tyr Gly Gln Gln Ala Gly Val LeuGln Glu Ala Arg 260 265 270 Val Pro Ile Ile Ser Asn Asp Val Cys Asn GlyAla Asp Phe Tyr Gly 275 280 285 Asn Gln Ile Lys Pro Lys Met Phe Cys AlaGly Tyr Pro Glu Gly Gly 290 295 300 Ile Asp Ala Cys Gln Gly Asp Ser GlyGly Pro Phe Val Cys Glu Asp 305 310 315 320 Ser Ile Ser Arg Thr Pro ArgTrp Arg Leu Cys Gly Ile Val Ser Trp 325 330 335 Gly Thr Gly Cys Ala LeuAla Gln Lys Pro Gly Val Tyr Thr Lys Val 340 345 350 Ser Asp Phe Arg GluTrp Ile Phe Gln Ala Ile Lys Thr His Ser Glu 355 360 365 Ala Ser Gly MetVal Thr Gln Leu 370 375 3 21784 DNA HUMAN misc_feature (1)...(21784) n =A,T,C or G 3 ctgggaataa aatccctttt cctgtgccac caggcctccc cagctggccccagccttggt 60 tcccactacc ttccccaagc tctggccatc tggccatctc gatggcctctccagcctctg 120 acataagaga gcctgcttat tcttgcctca aggcctttgc ctgtgctgttccctctgccc 180 acagtgccct tccttgtggt ctgtgtgtgg ctggcacctc acctttcagagcttagctca 240 gaagtctcct ctaggggagg ccctgtgatc cctgatcccc tgcagaagcccacctgctgc 300 cccagcctgc acggttttct tcacagcctc tgccacaatc tggaaattattgggttcatt 360 tacttgtttc cttgttaatg tctcccactc cccacctaca cgcatgagaacgtgaacccc 420 tgagagtcgt aaccttatct gtcttctttg ggttatgttc ccggaacctagaaaggtgcc 480 aagcacacag cggatgttca gtaggatggt aaacaaataa agcttctttaggctgatgaa 540 aaaactgagg gtcaggcgcg gtggctcacg cctgcaattc caacactttgtttgggaggc 600 tgagacaagc agataacttg agtctgggag ttcacgacca gcctggtcaacatggcaaac 660 cccgtcaata caaaaaatac aaaaattagc catgtgtggt ggtgtgcgcctataatccca 720 gctactcggg aggctcagaa ttacctgagc ctgagcgctt gagactgcagtgtgccatga 780 tcgcgccgct gcactccagc ctgggcagca cagtgaaacc ctgtctcaaaaaaaaaaaaa 840 agaaaaagaa aggagagaga gagagaagaa agaaagaaag aaagaaagaaagaaagaaag 900 aaagaaagaa agaaaaaagg aaggaaggaa ggaaggaaaa gaaaaaaactgaggctgagg 960 ctcagagagg ggaggggagt tgctcaggcc cacacatctc tgatgatttataaagcattt 1020 atagagaact tgctatgtgc caggcacttc cgcacagtga gagccaggatggcttcgtgg 1080 ctgtacacag gggacctggc atcaaacctg cccagggttc tggacgctgctctgcctctt 1140 ccaggctgtc actgtgggca cgtgacccca cttctctgag ctatctcaaaaacaggaatc 1200 atagttgtgg gattgaaata aggactaaat gagctgatgt atttagaacggtgcttagca 1260 cctggaggca tcaatacaat ttgagctatt cttcttcttc ttgaaaataactttaaatta 1320 ttatttttag aagtaggtgc tcagtggatg cccatttaat agataagaaagttgaggctc 1380 aaagatatga tggcacctgc cttaggttcc agctaggaag gggtagggtcaatattttta 1440 aatgaggctg gccagacgca gtggctcact cctgtaatct cagcattttgggaggctgag 1500 gaaggaagat cgcttcagcc caggagtttg agaccagcct gggcaacatagcaagaccac 1560 gtcgctaaaa aaattaatac ataaaataaa atgaggctgg cagattttcaagtggagggg 1620 caaatttgat cttgcaactg ggtaccatga gagaggtctg atttagggggtatctagggg 1680 caaagcatct agaacagcag aaacgactga ggcagcgagg aaatgccagcggcagggaag 1740 agagctacca agagggcaaa ggttgggggt cacagtccca agaagagatggcccaaagca 1800 aagacagaaa tacaaaagca cagtgtcact ggggaggaga cattccctaagtgccccaag 1860 gaaaacgtga caggcggtcg ggannnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 1920 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 1980 nnnnnnnnnn nnnnnnnnnn aataagttag ccctgggggc agggcagactggcctcgggc 2040 ccagaccctg ccgcaatgag gacaggcctg gctgtggccc cagcatggtgtctgttgcag 2100 gtggccggac tgtgccatgc tgctccagac ccaaggtggc agctctcactgcggggaccc 2160 tgctacttct gacagccatc ggggcggcat cctgggccat tggtgagagcggttcctgtg 2220 cctctgacct cccctggccc ctgcagcctc cagcctgcct gccctcacccctcccttctc 2280 tgcagtggct gttctcctca ggagtgacca ggagccgctg tacccaggtgagtggagcag 2340 gctgggaccc tctgggggag ccctggagga cacgtgtatc tggcgggagctcaacaagcg 2400 tatttgttga ataaatgcac aaatgcatgc agaaatgcta atcataatagtgcatttgta 2460 ttgagtgcct gctatgtacc aggcactatt ctaagcaccc cacatgtctaacccagactt 2520 tttcagacac cagtgtatta ctcatgagtg cctcataaaa ttaaattagtgagttggaaa 2580 accatgtttt ttttttaagt atgaaataga ttcgattaca gactatcacagtacatctct 2640 cagtaagtaa aggttatgct aatttttgtt tgtttttttt ttttttgcatccatatacat 2700 gtaatcccac tgcatcccca cactctgagg gtgggactgt tattctccctgttttacaga 2760 tggggaaact gaggctttga gcaatgcggc agtttgcccc agactacagagctatgggct 2820 acatcaggat gtaaaaatgt gtttcttact gcgtggcatg gtgaaaacatgttggggagg 2880 catgatataa attcagtgga cccttctaac tctcctagga ggtagtttttttgtttgttt 2940 gttttaaaaa agaaaaaagt cttgctctgt cacccaggct agagtgcaatggtgcagtct 3000 cagctcaccg caacctctgc ctcccaggtt caagcgattc tcctgcttcagcctcccaag 3060 tacctgggaa tacaggcgtg tgccaccatg cccagttaat tttttgtatttttagtagag 3120 atgagatttc accatgttgg ccaggacggt ctcgatctcc tgaccttgtgatccacccgc 3180 ctcagcctcc caaagtgctg ggattacagg catgagccac tgcgcctgtccctggtatta 3240 gctccatttt acagatgtgc aaaatgagga ccagagagga catgcagctggggaacgagg 3300 ggccaggaac agctcttaga cttatccact gtaagtgtgt ctgcaggcatgtggaatgaa 3360 tggccacaca aataaataga taaagaaact aactgtggga tgaatgaatgaatcttccca 3420 aatgccaact tcaagctgcc attccctgat gcaggacagc aggaaaaaaggggaagttgg 3480 gtggtgggat gtatttttca tgtctgtgag cctcatctaa ttccataaaggattcagttc 3540 acactaaaat cagaaatgaa aatccagaca agaaaagcca acatcaacattaatcatcat 3600 taccagcact tagcatttgt atgcaccagc caaggccttg ggaccttatgatatcaactc 3660 attaagtctt cccaacaacc tgttgttttt cttttctttt ttttttctttctttctttct 3720 ttcttttttt tttttttttt ttgagatggg gtcttgctct gtcgcccaggctggagtgca 3780 gtgacacgat cttagctcat tgtaacctac atctcctggg ctcaagcaatcctcccatct 3840 cagccttctg agtagctggg actataggct aatgccacca tgcctacacaaaattatttt 3900 gtcaataaca aattattgtt atttttatct ttttgagcca gagtctcgctgtgtcgccca 3960 ggcaggagtg ctgtggcgcg atcttggctc actgcaatct ccatctcccaggttcaagtg 4020 attctcctgc ctcagcctcc tgagtagcta ggactacagg cacgtgccaccacacccagc 4080 taatttttgt atttttagta gaggcggggt ttcaccatgt tggccaggatggtctcaaac 4140 tcctgacctc aggtgatcca cccgtctcgg cctcccaaag tgctgggactacaggcatga 4200 gccaccacac ccaacctcat tttttaaatt tttagtagag atgggatcttgctacattgc 4260 ccagtctgat cttgaactcc tgagctcaaa gcagtcctct cagatcagcctcccaaagtg 4320 cagggattac aggtgtgcac caccacaacc cattttccta tggggatgctgaggcacaga 4380 aaggctgagt gacttgcccc aggtcatgga gctagtcagt gtcagggctgggatttgaac 4440 ccaggcagcc tgcgtagtaa ctgtatatag tgtctacact tgattgcttgttaaaaaaaa 4500 aaaaaagaac agctgaattc attgccatag taaagactga catatgccaggccctggcgg 4560 cagcctttac ccagcaggcc tatgaagtta gggctgttac atcccaacattttgcatttg 4620 ggggaaattg agtcccagtg aagcaaactg acttgcccga ggctgaccacacatcagaga 4680 cagagcgaag ggatcacgcc cctgtcaaaa gcccctccgt gacaacacgtggcattgaga 4740 taaaatccca acccatcaca ggctccaagc ctcctagtgt ggaggcccctctccaccccc 4800 acctcacact ggcttctagc accctcaggg cccagtccct tgctcaaatgacctgctcac 4860 acagaagtct ctactcaccc acttctttct agctcacacc cagaggcagatttcagttct 4920 gcacagttcc ttctgagctg tggggcctcc caccagtccc tactctctccaagactcaat 4980 ttcctcatct gtgagatggg ggtaagaaga atcagtggga ataagaggagataaaaatct 5040 gtgtagtact tgggcggggt gcggtggctc acccctgtaa tcccagcactttgggaggcc 5100 gaggcaggca gatcacctga ggtcaggagt tcgagaccag cctggccaacgtggtgaaac 5160 ctcatctgta ctaaaaacac aaaaattggc caggcgtggt ggcgggcgcctgtaatccca 5220 gctactcagg aggctgaggc aggagaactg tttgaacctg ggaggcgcgggttgcaggtt 5280 gcagtgaact gagatcacgc cactgcactc cagcctgggt gacagagcaagagtctgtct 5340 caaaaaaaaa aaaaaaaaaa aggctgtgca gtacttgcct cttagccagcacagtggaca 5400 ttggcttttg tatctcactc ctgaaattct ttcttgaaat ttcttgagcaagatcttcct 5460 ggacttccag actctatggc ctctcaccct atggtgtgtc cctgccaccccggtaaaacc 5520 ctcctcactc attgtgaatt atttactcct ggcgaactcc aggaaggcagggaccttttg 5580 tggtcagacg gtgcctggca catagtaggt tctcaggaaa tccttgagttatgagtgcac 5640 ccaaagccaa aacactggga tgaactagag agtcatgggc ctccagctggaaaggagcga 5700 ggccaccact cacaaccggc tctggccagc accacgccgc caccctgcagaggtatttgg 5760 gtttttcaac aactcaggga aatgatgaaa caaacaaaca aacaaaaacaaccccaagct 5820 tgtatcccca cctcgctttt tttttcctgg gattttcaca cttctaaatatatccaacaa 5880 cttggcaggc acaccaggtg acccagaaca tcctttttgt gttgcctgaaatgataggaa 5940 caagaataaa gaatttaaaa gtgagaaaca gcagcagaga gtgtgactttaaaaatagcc 6000 agaggggaca tttgatgttc tctccccact cccatctccc ccaacacacatctataaagt 6060 gattttcccc cctaaaacct cacactttct ggaaatcaca tttccagagcagttaacagt 6120 cattttaaaa taagaatcca cccctcttcc tgccccagct ggtgtttcaaactccaagcc 6180 ttggctttca tggggtgatg aggacccccc agctagaggt gccaggcattccctgcccca 6240 accccagagc aggagaccgt aattaaggca ggccaggccg gtgcggtggctcacgcctgt 6300 aatcccagca ctttgggagg cccaaatggg cagatcactt gaggtcaggagaccagcctg 6360 gccaacatgg caaaacccca tctctactaa aaatacaaaa attagccgggcgtggtggct 6420 ggtgcctgta atcccagcta tttgggaggc tgaggcatga gaatcgcttgaactcaggag 6480 gcagaggttg cagtgagctg agatcgtgcc actgcactct agcctgggagacagagcaag 6540 actccatctc aaaacaaact taaaatagaa taaaataaaa taagaatccgcccccctccc 6600 cgccccagtt ggtgtttcaa accctgagac ttggccttgg aattcatggggtgatgagga 6660 ccccacagcc agaggtgcca ggcgttccct gccccaaccc cagagcaggaggccatcatt 6720 aaggcaggcc agccaggtgg cttttcagtg ccagccgtag ctgaatatattaggcaggga 6780 gacaggcaag ggtttgtatg agacccacag aaggaacagg gaatatgctggtctgggttc 6840 aagtcccggt tttgctggtt agccgtgtgc ctctgggcaa gtttattcctctgaggctta 6900 gttttcccat ctgtaagatg ggcatagaag tggtcactac tggctgggcacagtggctca 6960 cgcctgtaat cccagcactt ggggaggcca aggcaggtgg atcacctgaggccagaagtt 7020 cgagaccagc ctggccaaca tggtgaaacg ctgtttctac taagaacacaaaagttagcc 7080 aggtgtagta gcatgtgcct gtaatcccag ctactcggga ggctgaggcaggaggatcgc 7140 ttgaacctgg gaggcagagg ttgcagtgag ccgagatcat gccactgcactccagcctga 7200 gcaacagagc aagattatgt ctcaaaaaaa aaaaaaaaaa ccgaagtggtcactatctcc 7260 gaggatggtt gtgggattca gagagccact tggataggat gcatagcatggggccagccc 7320 actgacaccc cccagtaaac gtagccagtg ctattattac tgtgctgttgtttaaccctc 7380 cagaggggaa gtctcttgag aggctgtcca gggcaatgtt aaaagcttggggtttgaagt 7440 cactcagacc tgatttcgaa tcctctctcc ctgcttctcg tgcatttggtgacgttgggg 7500 aagccacccc acctctctga gcctcagctt ccccgtctgg aatttggggatgatcttcgt 7560 ggctcctggg gtgtgcgacg aggccttggt tgatggtggg gcagaggtagcctagcccca 7620 ggaacacagt aggtcctcag ctggggagag ttctacttgg aagtcttgcttctccttgtc 7680 ccaacctgcg gggctgtggg aagacccctc agctggtgtg tggcctcaccaggttccttc 7740 taagaggatg caaaagcaag ttttcatttg actcggtttc ccagaatgtgctctcagagc 7800 ccaggccagg caggaggctc ttgagaaaag gacaaaaaga catggtggctcacacctgcc 7860 atcccagcac tttgggaggc caaggtggga ggattgcttg aggccaggagtttgagatca 7920 gcctggacaa tatagcaata ccctgtctct acagaaaaaa ataaatttaaaaggcgtttt 7980 tagctcaggc tttgctgggt tctaacctgg ctattgtcac tcagctttatcctaacataa 8040 aaaaataaac aaattagcag ggtgtggtgg tatgcccctg tggtcctagctacttgggag 8100 gttgaggcgg gaggatcgtt tgagcccagg aggttgaggc tgcaatgagctatgatcgtg 8160 ccactgcact ccagcctggg tggtggagcg agaccctgtc tcaaaaaagaaaaaaaaaaa 8220 gtggcaggga gaaggaaagg aaaggacaaa gaggttcaca gctgatctctccctgaacct 8280 gctccttccg tccccatctc tgtcagcccc atcttttcag gctcaggccaaacccctcgg 8340 ttaccctccc agttcctcca gtcacccatg aatcagatct tgcaggaaaccctgtcagct 8400 gcacctacag aacctctcca aaatctgaac tcttctcccc gtccactgcccccaccctgc 8460 tccagccccc ttcccctccc ctctggacat cccagagcct cctccctggcctccctgctc 8520 ccatccctgc cccccaatca tatcccacaa aggggatatg actcactcacttaaccggca 8580 attctggagg gtcttaaaac ctggctgcct caagaggctt taaaatgttatcagatgggg 8640 gccaggtaca gtggctcatg ctggttcccc acttgcagcc agagggagctggtgaccacc 8700 tgagtcaggt cagggccctc ccctggctgc acctcacacc aggtgccagcaaagccctga 8760 tgttgctcta tttctagctc ccacctgatc tgcccctccc tggctcactctgctctggcc 8820 tcccactgtt cctggagcac tccccccagt cccccacacc agccttgggatctttgcatc 8880 tgcaagtccc tctgtctccg tgctgatctc acacacctcc tgacactttctcacctcctg 8940 caggtctttg ttcctgcacc accttcccag ggacgctctc cttgcagcgactgaaaagtg 9000 caacctcacc ccaccctcca caccggcact cccctccctc ggtggcattttatttttctc 9060 tgtggcccct tcctatcttg tgacacataa tatatcctac ttatttgtccctttcttgat 9120 ttgtctcacc tactgagctt tgagttccac aggggtcggg gtttttgtctgatttgttca 9180 ttgcagtggt gatttgttca ctgcctaaaa tagagcctgg caggtacaaagtgtttggta 9240 aatagaaatc aataccccag ggtctgtgac ctgacttagg tgttaacaggttcctctgag 9300 gtgtgtgggg aacagactga ggggtttcag gggacatctg ttctcaccacaaattgcccc 9360 ccaaccagcc ccagacatga acagtctccc gggagctccc tctagccttctcgtatatcc 9420 cagccctgcc tcatgtcaca atttgtaatg atgtgtttgg ctgggtgacattttatggcc 9480 atctgtctcc ctatccccta taatgtggtt tgccgaaagc aaagcccaggactgtctcgg 9540 ccatctgtgt ctccaggatc acccctcact gggcatggag tatgtgtccagttaacgctt 9600 gctgagtgaa tgaatgaata ctccatcctc tgcctggaga attacgcactttagcatatc 9660 caaggctctg acaagtcctg cataaaagag cattattgtt ttctttctttctttccttct 9720 ttccctcttc ttttctttct gactatagga tattgattat caatctggcaatagtcaaga 9780 ttggcagtct ggtgtattag tcaaaggttt tcagcctaca aaagacaaaaagaaaaaata 9840 aactggctaa aaacaaaagg ggatatgatt tactaactca cttaaccgacagtcacagag 9900 gttcttcaaa cctggctgta tcaaggggct ttaaaatgtt atcagatgggggccaggtgc 9960 agtagctcac gcctgtcatc cagcactttg ggaggccaag acaggcagatcacttgaggt 10020 caggagttcg agaccagcct ggccaacatg gtgaaacccc gtgtctactaaaaatacaaa 10080 aaattagcca agtgtggtgg catgtgtctg tagctccagc tactcgggaggctgaggcag 10140 gacaatggct tgaatccggg aggcggaggt tacagtgacc caaggttgcaccagtgcatt 10200 ccagcctggg tgacagagcg agactctgtc tcaaaaaaaa aaaaaaagttatcagatggg 10260 aaatgaattc cgatattaaa aattgatatg tatttatact atattattaaagttattttt 10320 cataaaacat agaagggtaa gtttaagaaa tgagaagtat ttataccaaaatgattaaat 10380 attatttaat ttaaagatat aaatgtcttg ttggacaaat aattcaaaatttccattaga 10440 caggaaaaat aagttcaaga gatatattga acaacatggt gattatagttaataacaata 10500 tattatatac ttgaacattg ctaaaagata ttttaagtgt tctcaccacacacaaagggt 10560 agtgcatgtg ttaattagct tgatttagcc gttccacaac gtatacatatttcacatcat 10620 cttgtacacc atcaatgtat ataattttgt caattaaaat aaatacatattttaaggccg 10680 ggtgcagtgg ctcacaccta taatcgcagc actttgggag gccgaggcaggcagatcacc 10740 tgaggtcagg agtttgagac tagcctggcc aacatggtga aaccccattctctacttaaa 10800 atacaaaaaa attagctggg catggtggtg catgtctgta atcccagccactcgggaggc 10860 tgaggcagaa gaatcgcttg aacccgggag gcagaggttg cagtgagctgagattgcacc 10920 actgcacacc agcctggaca acagaagtga gactccgtct caaaaaaataaataaataaa 10980 aataaaataa atacatatat atttttgaga tggagtctca ctctgtcgcccaaactggag 11040 tgcagtggca cgatcttggc tcactgcaac ctctgctgcc caggttcaagcaattctcct 11100 gcctcagcct cccgagtagc tgggattaca ggcacctgcc atcatgcctggctaattttt 11160 gtagttttca tagagacgag gtttcatcat cttggccagg ctggtcttgaactcctgacc 11220 ttgtgatcca cccatctcgg cctcccaaat aaatacatat tttaaaagatagaaatcact 11280 ctggaaggag agttaatctg tttgatataa taataatata ttaatattatattataacaa 11340 tatattagta ttatattcta ataatatatt aatattatat tataataatatattattata 11400 ttataacaat atattaatat tatattataa caatatatta atattatattatgtaataat 11460 actactactc catatagcta tggaaaagtt catatgaaga aaccaggctatgatctacaa 11520 actggcaaca aatttgttct tctattttcc atatgctgtc tgtgtacgtataaagtgaga 11580 ggtcttttta tatgagttaa gggtgtgacc aaagacaaat ggaaaaagacaaatgacaaa 11640 catactaata aagagcttcg gtttctccac aaaaaataca ataataaaataaaatgttat 11700 cagaaatctc ttgactctcc tccacgttag ctcacttttt ccctcaagagggtgaacatg 11760 acccttaaca gatccagcct caagtgctgg attctcttgg gaacttggttaaatggtttt 11820 ttttcttccc gaatgtccaa gtcaccttcc agacctgcag ctcctgagcagccaacttag 11880 gacttctaat ggagagtgaa gttcccctgg ttcgcggagg ggccggccacagcctcaagg 11940 ctgctgttga ttggtccgac ctgagtcctt gagtctggca gagtgccatggtgctctgta 12000 atcccacctg taatcccagc attttaggag gcagaggcag gaagattgcttgagcctagg 12060 agttcaagac cagcctgggc aacatagcaa gacccgtctc tacaaaacaaaacaaaacaa 12120 aacaaacaaa caaaaaaatt agccaggtgt ggtggtgcac gcctgtggtcctagctactc 12180 aggaggttga ggtaggagga tttcttgagt ctgggaggtc aaggctacagtgagccaaga 12240 tcacaccact acactccagc ctgggcaaca gagcgagacc ctgtctttaaaaaaaaaaag 12300 tccttgagtc atgattccag atgcaatcgc agatgtgggg gctgcaaccctccgatgggc 12360 tggggttcac gtctacacca catggctgga gcacaggcca ggaggggctccggctgggga 12420 agcatgtggg gagcctggct gtgggaccca ggcggccccg ggccctgtcgccctgcagtg 12480 caggtcagct ctgcggacgc tcggctcatg gtctttgaca agacggaagggacgtggcgg 12540 ctgctgtgct cctcgcgctc caacgccagg gtagccggac tcagctgcgaggagatgggc 12600 ttcctcaggt actgggggcc ctcggagggg tgggagccgg gaggggctggggagcaggcc 12660 taacccctgc cccgcccagg gcactgaccc actccgagct ggacgtgcgaacggcgggcg 12720 ccaatggcac gtcgggcttc ttctgtgtgg acgaggggag gctgccccacacccagaggc 12780 tgctggaggt catctccgtg tggtgaggag ggcagcgggc aggtggggcaacacctcaga 12840 cccccaaggc actccctctc cccgttttcc ttccacctgt cttaactggtctctatttcc 12900 tttctttctg tgtctccaat cccatctctc ccagtgattg ccccagaggccgtttcttgg 12960 ccgccatctg ccaaggtgag atcctaaaac tcagaaccct ctcctttaggcccttgggga 13020 ggccacgtcc cctcaagctc cccaggatgg ggccatgtac tttcagaccccctagggcag 13080 ggccaagcct gggctctggg gacctgggct ccagtcccct gtcgccgccccctgctgacc 13140 cttgtcccac agactgtggc cgcaggaagc tgcccgtgga ccgcatcgtgggaggccggg 13200 acaccagctt gggccggtgg ccgtggcaag tcagccttcg ctatgatggagcacacctct 13260 gtgggggatc cctgctctcc ggggactggg tgctgacagc cgcccactgcttcccggagt 13320 gagtgccccc caatggcgct gatgatgggg aggcagagga gcggagagacagtggggagg 13380 agggcggatt gtgcccaggc aggtggccac cctccacccc tttccctggtaggcggaacc 13440 gggtcctgtc ccgatggcga gtgtttgccg gtgccgtggc ccaggcctctccccacggtc 13500 tgcagctggg ggtgcaggct gtggtctacc acgggggcta tcttccctttcgggacccca 13560 acagcgagga gaacagcaac gatattgccc tggtccacct ctccagtcccctgcccctca 13620 caggtaagtc taagggctga gccatggggc ttgaggaccc gaggccaggaggacagagga 13680 ggggaccagg ggcacaaggc aatcaactta tggctcaggc atccttggcaataaggggaa 13740 tgatctcgag ggagcacaaa gtgggcctta actatcaatg atcagtgcagccaatttgga 13800 aaatttgcca gcatttcccc aagaagtata cataaagtta ccattggacccaacacttcc 13860 actcccagga caggaggtat atacctaaga caaatggaaa ctgtgtctgcaccaaaactc 13920 gtacatcagt gttcatagca gcattattca taatagccca aagatggaaacagcccaaga 13980 gtgtttcatc ggacaaatgc ataaagaaaa tgtggtatat tgaccgggcgcggtggctca 14040 tgcctgtaat cccagcactt tgggaggccg aggtgggtgg atacacgaggtcaggagttt 14100 gaaaccagcc tggccaacat ggtgaaactc ctctctacta aaaatacaaaaattagnnnn 14160 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14220 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14280 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14340 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14400 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14460 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14520 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14580 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14640 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14700 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14760 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14820 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14880 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 14940 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15000 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15060 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15120 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15180 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15240 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15300 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15360 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15420 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15480 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15540 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15600 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15660 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15720 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15780 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15840 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15900 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 15960 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16020 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16080 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16140 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16200 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16260 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16320 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16380 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16440 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16500 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16560 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16620 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16680 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16740 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16800 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnnnnnnnnnnnn 16860 nnnnnnnnnn nnnnnnnnnn nnnnnnttgc cacacccttc tccttagtgaaaagtagtga 16920 gagagttaat attgaagtaa ggacgcatct ttgaggacag gtggacaggtggaagcggct 16980 gggatttcag acacagggct gagggggtca cagcatgggc tttggggtcagattcagata 17040 tttgccaact gtgtgatctt ggacacatga cttcacctca ccgtgtctcagtttccctta 17100 tctgtaaaat gacttcctag ggttattgag acaattaaaa gggttaatatgagtaaagag 17160 cttagagaac tgccagcaca tagtgaacac tggtaaatgt tagcaattgctactattgtt 17220 gtttaatact tttactagtt atatgaacac ttgctgtttg cctggcatgcaactcaatga 17280 ctcaccaatt tctcactaca acttctgggg ataagtgatt attatttccattctacatct 17340 gagagctcta agactcaggc aggtgatgtc atcagcaggc agcaggcaacaggcagggct 17400 gccaggaacc cttgcatagg ttgtgcactg cacaaggaca ccacatctcagggttaccac 17460 tctctctgta gacctgtgta tttattatta tgattttctg ccaggtggaagtcaaatgtc 17520 tcaagatagg agtgtctctc tctctctctc tctttcttct ctctctctctttcttttttt 17580 gagacagagt cttgctctgt cacccaggct ggagtgcaat ggcgcaatctcggctccctg 17640 caaactctgc ctcctaggtt caagcgattc tcctgcctca gcctcctgagtagctgggat 17700 tacaggcacc tgccatctgt aatcccagtg ctttgggagg ctgaggcaggaggattgctt 17760 gagcccagga ggccgaggct gcagtgagcc atgttcctgc cactgcactctggcctgggt 17820 gacactgcag gcttagaaat gaaaacaagc tgtgttaaaa catacatgttatgaaacttt 17880 ggacacgtga cttggcctca ttttccccct ctctaaaatg ggataatatagaccctacct 17940 ctctgggctg atgaaacatt aaagaaaatg gtgcaggaag gcgcctagtatgcgatgagc 18000 tcttggtacg tggcgacttc cgttgtggct tttttgtttg tttgtttgtttttgagacag 18060 agtcttgctc tgtcgcccag gctggagtgc aatgacatga tctcggctcactgcaacctc 18120 cacctcctgg gttcaagtga ttcttctgcc tcagtctccc gagtagctgggattacaggt 18180 gcgtgccacc atgcccggct aatttttgta tttttagtag agatgaggtttcgccatgtt 18240 ggccaggctg gtctcaaact cctgacatca agtgatcctc ctgcctcggcctcccaaagt 18300 gctggtatta caggcatgag ccactgtgcc cagcctattg tggttttttttttaaagaac 18360 agagagggca gggtgtgtta ggggccatgg tagcagctgg acagaggtttgtaccaggtg 18420 gggcaggcca gcaggggctg gaccagcatt gtctctctca cagaatacatccagcctgtg 18480 tgcctcccag ctgccggcca ggccctggtg gatggcaaga tctgtaccgtgacgggctgg 18540 ggcaacacgc agtactatgg tgagtcctgt cctctgcctc tgatgccaccatttgggaga 18600 ctctgaactg ggctggggat gggcagtctg gctggttgga tgagtcttgaccatgaggag 18660 tagggatgct gaggggaatg gggtgggcac caggagggaa ggggggtgtgtacacccccc 18720 agctctggcc agccttgcct gcacaccccc aggccaacag gccggggtactccaggaggc 18780 tcgagtcccc ataatcagca atgatgtctg caatggcgct gacttctatggaaaccagat 18840 caagcccaag atgttctgtg ctggctaccc cgagggtggc attgatgcctgccaggtgag 18900 ggactctgta ggggcagccc cctggtcgct gccaccccag ggatggagacgcaggggagt 18960 gggtggtcgg gctccccatc taaaagcctg agggctctgg ggccacagcccatgtcatcc 19020 cgggggggcc tcctgtctaa ccactttggc ctccagccag acctccctctcccctcccag 19080 ggcgacagcg gtggtccctt tgtgtgtgag gacagcatct ctcggacgccacgttggcgg 19140 ctgtgtggca ttgtgagttg gggcactggc tgtgccctgg cccagaagccaggcgtctac 19200 accaaagtca gtgacttccg ggagtggatc ttccaggcca taaaggtgaaagttgggtcc 19260 agatgggagc cagggtgggg acgtttgggt gtctaatggg ggaagggaggcagagatttg 19320 ttttaggaaa cctacgctca ggcctagaag agggcccccc ttgggaacagatggactttg 19380 aagggttcct ggggaaggga agccagtggt gggacgtgga agcctctcagacctcgggag 19440 cccccagctg tctttcccca gactcactcc gaagccagcg gcatggtgacccagctctga 19500 ccggtggctt ctcgctgcgc agcctccagg gcccgaggtg atcccggtggtgggatccac 19560 gctgggccga ggatgggacg tttttcttct tgggcccggt ccacaggtccaaggacaccc 19620 tccctccagg gtcctctctt ccacagtggc gggcccactc agccccgagaccacccaacc 19680 tcaccctcct gacccccatg taaatattgt tctgctgtct gggactcctgtctaggtgcc 19740 cctgatgatg ggatgctctt taaataataa agatggtttt gattaatgtggcctccgagc 19800 ttacaaatgt acacagcaat gaggacattt tgtcaggaag gaagagaagaattaggacct 19860 ggcgcaaatc agacagagag tgtgggtccc tcagttccca ctgatttgagatttaagatt 19920 ttaattggtt cacttaactg gaattttcct ggagcaaatt ggcttcaggtacagctggat 19980 ccagctgctc tctcaaatct gccttaggct gtgttagctt catttccaagcagcctctcc 20040 tacaaccaga gagagagatg tccccttcca cacaaactct ttcccaatcactgcagaaaa 20100 agacccaggc aacaacaaca acaaaaaccc aggcccagct cccattgtacagatttgggt 20160 cacgtgctca tcccttggca aatcactgtg caccggatgt acgcggtaggggtggagcgg 20220 ggtggagtgg gaggagctag gccttcaaga atcgtgtgac ctgagtgtgggagtcccaaa 20280 ggaaataggg tgctatttcc agaagtggaa atagatgctc agtgagcaaaaaagacatct 20340 accttgaacc aacacggaaa acggggccct gtaaggtgga gatagggagacgctgggaac 20400 acagcctgag accctccccc aacccctttc tccatctggg cagcttctggggaggaaccc 20460 ccttctgtag agcctctgca gagcctcatg cagccccgat ggccaccagggggcactgct 20520 gccccaacat tgtgacacat taaggggttt cctgcctgga gtcagccgcatgttgctgaa 20580 aacctgctgt tctgctgaag aaaggctcag cgggggagcc tgttcaccatgactttaaat 20640 aataacaatt atcatacatc acccatggac cacagcttcc aagcaatttccttttttttt 20700 tttttttttt ttttttgaga cagagtttca ctcttgtctc ccaggttggagtgcagtggc 20760 gtgatcttag ctcactacaa cctccgcctc ctgggttcaa gcgattctcctgcctcggcc 20820 tcccgagtag ctgggattac aggcgtgccc caccacgccc agctgatttttgtattttta 20880 gtagagacgg gctgtcacca tgttggccag gctgctctcg aactcctgacctcaggtgat 20940 ccacctgcct cggcctccca aagtgctggg tgtcacgcgc atccatgtgaagagaccacc 21000 aaacaggctt tgtgtgagca ataaagcttt ctaatcacct gggtgcaggcaggctgagtc 21060 cgaaaagaga gtcagtgaag ggaggtaggg gtggggccgt tttatgggatttggataggt 21120 agtggaaaat tacagtcaaa gggggttgtt ctctggcggg caggggtgggggtcacaagg 21180 tgctcagtgg gggagcttct gagccaggag aaggaatttc acaaggtaatgtcatcagtt 21240 aaggcaggaa ccggccattt tcacttcttt tgtgattctt cagttacttcaggccatctg 21300 gatgtataca tgcaggcttg ggctcagagg cctgacactg ggattacagatgtctgctgc 21360 cacacctggc taatttttgt atttttagta gagacgggtt tcaccatgttggcaggctgg 21420 tctcgaactc ctgacctcag gtgatccgcc caccttggcc tcccaaagtgctgggattac 21480 aagcctaagc cactgcaccc agcccagctt cctaaaatat agatgatctacaagagctcc 21540 tttgagaaac tgacaaactg tgcatttgga aaacgatccc agcgtcactccccgatcccc 21600 acacccctgg cgaggttgag ccccaccact gctttgttgg tcaggagcccccaggcccac 21660 atcgtgttag cagagcctca gtgcagtttc cccaaacgtc tacctctggctgtggtgttc 21720 tacccatggc atgtgggatg taatttgaga cctgacctac ggcttgctttgttagaaacg 21780 tatt 21784 4 417 PRT HUMAN 4 Met Ala Gln Lys Glu GlyGly Arg Thr Val Pro Cys Cys Ser Arg Pro 1 5 10 15 Lys Val Ala Ala LeuThr Ala Gly Thr Leu Leu Leu Leu Thr Ala Ile 20 25 30 Gly Ala Ala Ser TrpAla Ile Val Ala Val Leu Leu Arg Ser Asp Gln 35 40 45 Glu Pro Leu Tyr ProVal Gln Val Ser Ser Ala Asp Ala Arg Leu Met 50 55 60 Val Phe Asp Lys ThrGlu Gly Thr Trp Arg Leu Leu Cys Ser Ser Arg 65 70 75 80 Ser Asn Ala ArgVal Ala Gly Leu Ser Cys Glu Glu Met Gly Phe Leu 85 90 95 Arg Ala Leu ThrHis Ser Glu Leu Asp Val Arg Thr Ala Gly Ala Asn 100 105 110 Gly Thr SerGly Phe Phe Cys Val Asp Glu Gly Arg Leu Pro His Thr 115 120 125 Gln ArgLeu Leu Glu Val Ile Ser Pro Ser Asp Cys Pro Arg Gly Arg 130 135 140 PheLeu Ala Ala Ile Cys Gln Asp Cys Gly Arg Arg Lys Leu Pro Val 145 150 155160 Asp Arg Ile Val Gly Gly Arg Asp Thr Ser Leu Gly Arg Trp Pro Trp 165170 175 Gln Val Ser Leu Arg Tyr Asp Gly Ala His Leu Cys Gly Gly Ser Leu180 185 190 Leu Ser Gly Asp Trp Val Leu Thr Ala Ala His Cys Phe Pro GluArg 195 200 205 Asn Arg Val Leu Ser Arg Trp Arg Val Phe Ala Gly Ala ValAla Gln 210 215 220 Ala Ser Pro His Gly Leu Gln Leu Gly Val Gln Ala ValVal Tyr His 225 230 235 240 Gly Gly Tyr Leu Pro Phe Arg Asp Pro Asn SerGlu Glu Asn Ser Asn 245 250 255 Asp Ile Ala Leu Val His Leu Ser Ser ProLeu Pro Leu Thr Glu Tyr 260 265 270 Ile Gln Pro Val Cys Leu Pro Ala AlaGly Gln Ala Leu Val Asp Gly 275 280 285 Lys Ile Cys Thr Val Thr Gly TrpGly Asn Thr Gln Tyr Tyr Gly Gln 290 295 300 Gln Ala Gly Val Leu Gln GluAla Arg Val Pro Ile Ile Ser Asn Asp 305 310 315 320 Val Cys Asn Gly AlaAsp Phe Tyr Gly Asn Gln Ile Lys Pro Lys Met 325 330 335 Phe Cys Ala GlyTyr Pro Glu Gly Gly Ile Asp Ala Cys Gln Gly Asp 340 345 350 Ser Gly GlyPro Phe Val Cys Glu Asp Ser Ile Ser Arg Thr Pro Arg 355 360 365 Trp ArgLeu Cys Gly Ile Val Ser Trp Gly Thr Gly Cys Ala Leu Ala 370 375 380 GlnLys Pro Gly Val Tyr Thr Lys Val Ser Asp Phe Arg Glu Trp Ile 385 390 395400 Phe Gln Ala Ile Lys Thr His Ser Glu Ala Ser Gly Met Val Thr Gln 405410 415 Leu 5 601 DNA HUMAN 5 aaaaggctgt gcagtacttg cctcttagccagcacagtgg acattggctt ttgtatctca 60 ctcctgaaat tctttcttga aatttcttgagcaagatctt cctggacttc cagactctat 120 ggcctctcac cctatggtgt gtccctgccaccccggtaaa accctcctca ctcattgtga 180 attatttact cctggcgaac tccaggaaggcagggacctt ttgtggtcag acggtgcctg 240 gcacatagta ggttctcagg aaatccttgagttatgagtg cacccaaagc caaaacactg 300 rgatgaacta gagagtcatg ggcctccagctggaaaggag cgaggccacc actcacaacc 360 ggctctggcc agcaccacgc cgccaccctgcagaggtatt tgggtttttc aacaactcag 420 ggaaatgatg aaacaaacaa acaaacaaaaacaaccccaa gcttgtatcc ccacctcgct 480 ttttttttcc tgggattttc acacttctaaatatatccaa caacttggca ggcacaccag 540 gtgacccaga acatcctttt tgtgttgcctgaaatgatag gaacaagaat aaagaattta 600 a 601 6 601 DNA HUMAN 6 tcactcctgaaattctttct tgaaatttct tgagcaagat cttcctggac ttccagactc 60 tatggcctctcaccctatgg tgtgtccctg ccaccccggt aaaaccctcc tcactcattg 120 tgaattatttactcctggcg aactccagga aggcagggac cttttgtggt cagacggtgc 180 ctggcacatagtaggttctc aggaaatcct tgagttatga gtgcacccaa agccaaaaca 240 ctgggatgaactagagagtc atgggcctcc agctggaaag gagcgaggcc accactcaca 300 mccggctctggccagcacca cgccgccacc ctgcagaggt atttgggttt ttcaacaact 360 cagggaaatgatgaaacaaa caaacaaaca aaaacaaccc caagcttgta tccccacctc 420 gctttttttttcctgggatt ttcacacttc taaatatatc caacaacttg gcaggcacac 480 caggtgacccagaacatcct ttttgtgttg cctgaaatga taggaacaag aataaagaat 540 ttaaaagtgagaaacagcag cagagagtgt gactttaaaa atagccagag gggacatttg 600 a 601 7 601DNA HUMAN 7 atagaataaa ataaaataag aatccgcccc cctccccgcc ccagttggtgtttcaaaccc 60 tgagacttgg ccttggaatt catggggtga tgaggacccc acagccagaggtgccaggcg 120 ttccctgccc caaccccaga gcaggaggcc atcattaagg caggccagccaggtggcttt 180 tcagtgccag ccgtagctga atatattagg cagggagaca ggcaagggtttgtatgagac 240 ccacagaagg aacagggaat atgctggtct gggttcaagt cccggttttgctggttagcc 300 rtgtgcctct gggcaagttt attcctctga ggcttagttt tcccatctgtaagatgggca 360 tagaagtggt cactactggc tgggcacagt ggctcacgcc tgtaatcccagcacttgggg 420 aggccaaggc aggtggatca cctgaggcca gaagttcgag accagcctggccaacatggt 480 gaaacgctgt ttctactaag aacacaaaag ttagccaggt gtagtagcatgtgcctgtaa 540 tcccagctac tcgggaggct gaggcaggag gatcgcttga acctgggaggcagaggttgc 600 a 601 8 601 DNA HUMAN 8 agtttattcc tctgaggctt agttttcccatctgtaagat gggcatagaa gtggtcacta 60 ctggctgggc acagtggctc acgcctgtaatcccagcact tggggaggcc aaggcaggtg 120 gatcacctga ggccagaagt tcgagaccagcctggccaac atggtgaaac gctgtttcta 180 ctaagaacac aaaagttagc caggtgtagtagcatgtgcc tgtaatccca gctactcggg 240 aggctgaggc aggaggatcg cttgaacctgggaggcagag gttgcagtga gccgagatca 300 ygccactgca ctccagcctg agcaacagagcaagattatg tctcaaaaaa aaaaaaaaaa 360 accgaagtgg tcactatctc cgaggatggttgtgggattc agagagccac ttggatagga 420 tgcatagcat ggggccagcc cactgacaccccccagtaaa cgtagccagt gctattatta 480 ctgtgctgtt gtttaaccct ccagaggggaagtctcttga gaggctgtcc agggcaatgt 540 taaaagcttg gggtttgaag tcactcagacctgatttcga atcctctctc cctgcttctc 600 g 601 9 601 DNA HUMAN 9 cctggctgcacctcacacca ggtgccagca aagccctgat gttgctctat ttctagctcc 60 cacctgatctgcccctccct ggctcactct gctctggcct cccactgttc ctggagcact 120 ccccccagtcccccacacca gccttgggat ctttgcatct gcaagtccct ctgtctccgt 180 gctgatctcacacacctcct gacactttct cacctcctgc aggtctttgt tcctgcacca 240 ccttcccagggacgctctcc ttgcagcgac tgaaaagtgc aacctcaccc caccctccac 300 rccggcactcccctccctcg gtggcatttt atttttctct gtggcccctt cctatcttgt 360 gacacataatatatcctact tatttgtccc tttcttgatt tgtctcacct actgagcttt 420 gagttccacaggggtcgggg tttttgtctg atttgttcat tgcagtggtg atttgttcac 480 tgcctaaaatagagcctggc aggtacaaag tgtttggtaa atagaaatca ataccccagg 540 gtctgtgacctgacttaggt gttaacaggt tcctctgagg tgtgtgggga acagactgag 600 g 601 10 601DNA HUMAN 10 gtatatccca gccctgcctc atgtcacaat ttgtaatgat gtgtttggctgggtgacatt 60 ttatggccat ctgtctccct atcccctata atgtggtttg ccgaaagcaaagcccaggac 120 tgtctcggcc atctgtgtct ccaggatcac ccctcactgg gcatggagtatgtgtccagt 180 taacgcttgc tgagtgaatg aatgaatact ccatcctctg cctggagaattacgcacttt 240 agcatatcca aggctctgac aagtcctgca taaaagagca ttattgttttctttctttct 300 ttccttcttt ccctcttctt ttctttctga ctataggata ttgattatcaatctggcaat 360 agtcaagatt ggcagtctgg tgtattagtc aaaggttttc agcctacaaaagacaaaaag 420 aaaaaataaa ctggctaaaa acaaaagggg atatgattta ctaactcacttaaccgacag 480 tcacagaggt tcttcaaacc tggctgtatc aaggggcttt aaaatgttatcagatggggg 540 ccaggtgcag tagctcacgc ctgtcatcca gcactttggg aggccaagacaggcagatca 600 c 601 11 601 DNA HUMAN 11 tatcccagcc ctgcctcatgtcacaatttg taatgatgtg tttggctggg tgacatttta 60 tggccatctg tctccctatcccctataatg tggtttgccg aaagcaaagc ccaggactgt 120 ctcggccatc tgtgtctccaggatcacccc tcactgggca tggagtatgt gtccagttaa 180 cgcttgctga gtgaatgaatgaatactcca tcctctgcct ggagaattac gcactttagc 240 atatccaagg ctctgacaagtcctgcataa aagagcatta ttgttttctt tctttctttc 300 cttctttccc tcttcttttctttctgacta taggatattg attatcaatc tggcaatagt 360 caagattggc agtctggtgtattagtcaaa ggttttcagc ctacaaaaga caaaaagaaa 420 aaataaactg gctaaaaacaaaaggggata tgatttacta actcacttaa ccgacagtca 480 cagaggttct tcaaacctggctgtatcaag gggctttaaa atgttatcag atgggggcca 540 ggtgcagtag ctcacgcctgtcatccagca ctttgggagg ccaagacagg cagatcactt 600 g 601 12 601 DNA HUMAN12 tccagttaac gcttgctgag tgaatgaatg aatactccat cctctgcctg gagaattacg 60cactttagca tatccaaggc tctgacaagt cctgcataaa agagcattat tgttttcttt 120ctttctttcc ttctttccct cttcttttct ttctgactat aggatattga ttatcaatct 180ggcaatagtc aagattggca gtctggtgta ttagtcaaag gttttcagcc tacaaaagac 240aaaaagaaaa aataaactgg ctaaaaacaa aaggggatat gatttactaa ctcacttaac 300sgacagtcac agaggttctt caaacctggc tgtatcaagg ggctttaaaa tgttatcaga 360tgggggccag gtgcagtagc tcacgcctgt catccagcac tttgggaggc caagacaggc 420agatcacttg aggtcaggag ttcgagacca gcctggccaa catggtgaaa ccccgtgtct 480actaaaaata caaaaaatta gccaagtgtg gtggcatgtg tctgtagctc cagctactcg 540ggaggctgag gcaggacaat ggcttgaatc cgggaggcgg aggttacagt gacccaaggt 600 t601 13 601 DNA HUMAN 13 tagttttcat agagacgagg tttcatcatc ttggccaggctggtcttgaa ctcctgacct 60 tgtgatccac ccatctcggc ctcccaaata aatacatattttaaaagata gaaatcactc 120 tggaaggaga gttaatctgt ttgatataat aataatatattaatattata ttataacaat 180 atattagtat tatattctaa taatatatta atattatattataataatat attattatat 240 tataacaata tattaatatt atattataac aatatattaatattatatta tgtaataata 300 mtactactcc atatagctat ggaaaagttc atatgaagaaaccaggctat gatctacaaa 360 ctggcaacaa atttgttctt ctattttcca tatgctgtctgtgtacgtat aaagtgagag 420 gtctttttat atgagttaag ggtgtgacca aagacaaatggaaaaagaca aatgacaaac 480 atactaataa agagcttcgg tttctccaca aaaaatacaataataaaata aaatgttatc 540 agaaatctct tgactctcct ccacgttagc tcactttttccctcaagagg gtgaacatga 600 c 601 14 601 DNA HUMAN 14 cacctcagacccccaaggca ctccctctcc ccgttttcct tccacctgtc ttaactggtc 60 tctatttcctttctttctgt gtctccaatc ccatctctcc cagtgattgc cccagaggcc 120 gtttcttggccgccatctgc caaggtgaga tcctaaaact cagaaccctc tcctttaggc 180 ccttggggaggccacgtccc ctcaagctcc ccaggatggg gccatgtact ttcagacccc 240 ctagggcagggccaagcctg ggctctgggg acctgggctc cagtcccctg tcgccgcccc 300 ctgctgacccttgtcccaca gactgtggcc gcaggaagct gcccgtggac cgcatcgtgg 360 gaggccgggacaccagcttg ggccggtggc cgtggcaagt cagccttcgc tatgatggag 420 cacacctctgtgggggatcc ctgctctccg gggactgggt gctgacagcc gcccactgct 480 tcccggagtgagtgcccccc aatggcgctg atgatgggga ggcagaggag cggagagaca 540 gtggggaggagggcggattg tgcccaggca ggtggccacc ctccacccct ttccctggta 600 g 601 15 601DNA HUMAN 15 gcaagtcagc cttcgctatg atggagcaca cctctgtggg ggatccctgctctccgggga 60 ctgggtgctg acagccgccc actgcttccc ggagtgagtg ccccccaatggcgctgatga 120 tggggaggca gaggagcgga gagacagtgg ggaggagggc ggattgtgcccaggcaggtg 180 gccaccctcc acccctttcc ctggtaggcg gaaccgggtc ctgtcccgatggcgagtgtt 240 tgccggtgcc gtggcccagg cctctcccca cggtctgcag ctgggggtgcaggctgtggt 300 ytaccacggg ggctatcttc cctttcggga ccccaacagc gaggagaacagcaacgatat 360 tgccctggtc cacctctcca gtcccctgcc cctcacaggt aagtctaagggctgagccat 420 ggggcttgag gacccgaggc caggaggaca gaggagggga ccaggggcacaaggcaatca 480 acttatggct caggcatcct tggcaataag gggaatgatc tcgagggagcacaaagtggg 540 ccttaactat caatgatcag tgcagccaat ttggaaaatt tgccagcatttccccaagaa 600 g 601 16 601 DNA HUMAN 16 ccctttccct ggtaggcggaaccgggtcct gtcccgatgg cgagtgtttg ccggtgccgt 60 ggcccaggcc tctccccacggtctgcagct gggggtgcag gctgtggtct accacggggg 120 ctatcttccc tttcgggaccccaacagcga ggagaacagc aacgatattg ccctggtcca 180 cctctccagt cccctgcccctcacaggtaa gtctaagggc tgagccatgg ggcttgagga 240 cccgaggcca ggaggacagaggaggggacc aggggcacaa ggcaatcaac ttatggctca 300 kgcatccttg gcaataaggggaatgatctc gagggagcac aaagtgggcc ttaactatca 360 atgatcagtg cagccaatttggaaaatttg ccagcatttc cccaagaagt atacataaag 420 ttaccattgg acccaacacttccactccca ggacaggagg tatataccta agacaaatgg 480 aaactgtgtc tgcaccaaaactcgtacatc agtgttcata gcagcattat tcataatagc 540 ccaaagatgg aaacagcccaagagtgtttc atcggacaaa tgcataaaga aaatgtggta 600 t 601

That which is claimed is:
 1. An isolated peptide consisting of an aminoacid sequence selected from the group consisting of: (a) an amino acidsequence shown in SEQ ID NO:2; (b) an amino acid sequence of an allelicvariant of an amino acid sequence shown in SEQ ID NO:2, wherein saidallelic variant is encoded by a nucleic acid molecule that hybridizesunder stringent conditions to the opposite strand of a nucleic acidmolecule shown in SEQ ID NOS:1 or 3; (c) an amino acid sequence of anortholog of an amino acid sequence shown in SEQ ID NO:2, wherein saidortholog is encoded by a nucleic acid molecule that hybridizes understringent conditions to the opposite strand of a nucleic acid moleculeshown in SEQ ID NOS:1 or 3; and (d) a fragment of an amino acid sequenceshown in SEQ ID NO:2, wherein said fragment comprises at least 10contiguous amino acids.
 2. An isolated peptide comprising an amino acidsequence selected from the group consisting of: (a) an amino acidsequence shown in SEQ ID NO:2; (b) an amino acid sequence of an allelicvariant of an amino acid sequence shown in SEQ ID NO:2, wherein saidallelic variant is encoded by a nucleic acid molecule that hybridizesunder stringent conditions to the opposite strand of a nucleic acidmolecule shown in SEQ ID NOS:1 or 3; (c) an amino acid sequence of anortholog of an amino acid sequence shown in SEQ ID NO:2, wherein saidortholog is encoded by a nucleic acid molecule that hybridizes understringent conditions to the opposite strand of a nucleic acid moleculeshown in SEQ ID NOS:1 or 3; and (d) a fragment of an amino acid sequenceshown in SEQ ID NO:2, wherein said fragment comprises at least 10contiguous amino acids.
 3. An isolated antibody that selectively bindsto a peptide of claim
 2. 4. An isolated nucleic acid molecule consistingof a nucleotide sequence selected from the group consisting of: (a) anucleotide sequence that encodes an amino acid sequence shown in SEQ IDNO:2; (b) a nucleotide sequence that encodes of an allelic variant of anamino acid sequence shown in SEQ ID NO:2, wherein said nucleotidesequence hybridizes under stringent conditions to the opposite strand ofa nucleic acid molecule shown in SEQ ID NOS:1 or 3; (c) a nucleotidesequence that encodes an ortholog of an amino acid sequence shown in SEQID NO:2, wherein said nucleotide sequence hybridizes under stringentconditions to the opposite strand of a nucleic acid molecule shown inSEQ ID NOS:1 or 3; (d) a nucleotide sequence that encodes a fragment ofan amino acid sequence shown in SEQ ID NO:2, wherein said fragmentcomprises at least 10 contiguous amino acids; and (e) a nucleotidesequence that is the complement of a nucleotide sequence of (a)-(d). 5.An isolated nucleic acid molecule comprising a nucleotide sequenceselected from the group consisting of: (a) a nucleotide sequence thatencodes an amino acid sequence shown in SEQ ID NO:2; (b) a nucleotidesequence that encodes of an allelic variant of an amino acid sequenceshown in SEQ ID NO:2, wherein said nucleotide sequence hybridizes understringent conditions to the opposite strand of a nucleic acid moleculeshown in SEQ ID NOS:1 or 3; (c) a nucleotide sequence that encodes anortholog of an amino acid sequence shown in SEQ ID NO:2, wherein saidnucleotide sequence hybridizes under stringent conditions to theopposite strand of a nucleic acid molecule shown in SEQ ID NOS:1 or 3;(d) a nucleotide sequence that encodes a fragment of an amino acidsequence shown in SEQ ID NO:2, wherein said fragment comprises at least10 contiguous amino acids; and (e) a nucleotide sequence that is thecomplement of a nucleotide sequence of (a)-(d).
 6. A gene chipcomprising a nucleic acid molecule of claim
 5. 7. A transgenic non-humananimal comprising a nucleic acid molecule of claim
 5. 8. A nucleic acidvector comprising a nucleic acid molecule of claim
 5. 9. A host cellcontaining the vector of claim
 8. 10. A method for producing any of thepeptides of claim 1 comprising introducing a nucleotide sequenceencoding any of the amino acid sequences in (a)-(d) into a host cell,and culturing the host cell under conditions in which the peptides areexpressed from the nucleotide sequence.
 11. A method for producing anyof the peptides of claim 2 comprising introducing a nucleotide sequenceencoding any of the amino acid sequences in (a)-(d) into a host cell,and culturing the host cell under conditions in which the peptides areexpressed from the nucleotide sequence.
 12. A method for detecting thepresence of any of the peptides of claim 2 in a sample, said methodcomprising contacting said sample with a detection agent thatspecifically allows detection of the presence of the peptide in thesample and then detecting the presence of the peptide.
 13. A method fordetecting the presence of a nucleic acid molecule of claim 5 in asample, said method comprising contacting the sample with anoligonucleotide that hybridizes to said nucleic acid molecule understringent conditions and determining whether the oligonucleotide bindsto said nucleic acid molecule in the sample.
 14. A method foridentifying a modulator of a peptide of claim 2, said method comprisingcontacting said peptide with an agent and determining if said agent hasmodulated the function or activity of said peptide.
 15. The method ofclaim 14, wherein said agent is administered to a host cell comprisingan expression vector that expresses said peptide.
 16. A method foridentifying an agent that binds to any of the peptides of claim 2, saidmethod comprising contacting the peptide with an agent and assaying thecontacted mixture to determine whether a complex is formed with theagent bound to the peptide.
 17. A pharmaceutical composition comprisingan agent identified by the method of claim 16 and a pharmaceuticallyacceptable carrier therefor.
 18. A method for treating a disease orcondition mediated by a human protease protein, said method comprisingadministering to a patient a pharmaceutically effective amount of anagent identified by the method of claim
 16. 19. A method for identifyinga modulator of the expression of a peptide of claim 2, said methodcomprising contacting a cell expressing said peptide with an agent, anddetermining if said agent has modulated the expression of said peptide.20. An isolated human protease peptide having an amino acid sequencethat shares at least 70% homology with an amino acid sequence shown inSEQ ID NO:2.
 21. A peptide according to claim 20 that shares at least 90percent homology with an amino acid sequence shown in SEQ ID NO:2. 22.An isolated nucleic acid molecule encoding a human protease peptide,said nucleic acid molecule sharing at least 80 percent homology with anucleic acid molecule shown in SEQ ID NOS:1 or
 3. 23. A nucleic acidmolecule according to claim 22 that shares at least 90 percent homologywith a nucleic acid molecule shown in SEQ ID NOS:1 or 3.